2309 lines
95 KiB
HTML
Executable File
2309 lines
95 KiB
HTML
Executable File
<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8">
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<title>Release Notes - MEME Suite</title>
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<link rel="shortcut icon" type="image/x-icon" href="images/memesuite_icon.ico">
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<link rel="icon" type="image/png" href="images/memesuite_icon.png">
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<link href="css/style.css" rel="stylesheet" type="text/css">
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<script src="js/menu.js"></script>
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</head>
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<body>
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<div class="memesuitelogo">
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<h1>The MEME Suite</h1>
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<h2>Motif-based sequence analysis tools</h2>
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</div>
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<h2>MEME Suite Release Notes</h2>
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<hr>
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<b>MEME version 4.11.2 patch 2 -- October 24, 2016</b>
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<ul>
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<li>
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<b>Bug fixes</b>
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<ul>
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<li>
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Fixed bug in handling of RNA-like custom alphabets.
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</li>
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<li>
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Fixed bug in MAST -comp option.
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</li>
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</ul
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</li>
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</ul>
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<hr>
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<b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
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<ul>
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<li>
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<b>Bug fixes</b>
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<ul>
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<li>
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Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate
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reading the sequence file.
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</li>
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<li>
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Modified MEME to fall back to a simple Dirichlet prior when
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using DNA or a custom alphabet with a prior that requires
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a prior library, but no prior libray is specified.
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</li>
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</ul
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</li>
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</ul>
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<p>
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<hr>
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<b>MEME version 4.11.2 -- May 5 2016</b>
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</p>
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<ul>
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<li><b>Enhancements</b>
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<ul>
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<li>
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Reduced running time of DREME by 60%.
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</li>
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<li>
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Improved running time of FIMO.
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</li>
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<li>
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Added Ensembl Fungi, Ensembl Metazoa, Emsembl Protists, and
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Ensembl Plants to on-line sequence databases.
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</li>
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<li>
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Improved links to on-line annotations in MAST results.
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</li>
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<li>
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Added <code>fasta-re-match</code> script for scanning FASTA files
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with regular expressions.
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</li>
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<li>
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Updated installation guide.
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</li>
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</ul>
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</li>
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</ul>
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<hr>
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<p>
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<b>MEME version 4.11.1 -- Jan 15 2016</b>
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</p>
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<ul>
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<li><b>Bug fixes</b>
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<ul>
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<li>
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Script tag 'src' attributes for web applications now include
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a 'version' parameter to prevent outdated scripts from being cached.
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</li>
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<li>
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The C standard <code>gnu89</code> is specified for the build.
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This resolves problems building the MEME Suite with GCC 5.1.
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This was a common problem for users running the
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latest version of Ubuntu.
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</li>
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<li>
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Fixed incorrect formatting of E-value threshold in MEME XML output.
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The incorrect formatting caused failures in <code>meme_xml_to_html</code>.
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</li>
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<li>
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Fixed error in TomTom web application when the RNA alphabet was
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selected.
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</li>
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<li>
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Fixed error in Javascript alphabet parser.
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The parser was not allowing blank lines,
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or lines consisting only of a comment.
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</li>
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<li>
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Fixed error in fasta-center and psp-gen scripts that prevented use of RNA
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alphabet.
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</li>
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<li>
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Fixed errors in specification of options, and parsing errors in
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elm2meme script.
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</li>
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<li>
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Removed broken link to LAM MPI.
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LAM MPI has been superceded by Open MPI,
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and the host web site no longer exists.
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</li>
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</ul>
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</li>
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</ul>
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<hr>
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<p>
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<b>MEME version 4.11.0 -- Nov 23 2015</b>
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</p>
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<ul>
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<li><b>New Features and Enhancements</b>
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<ul>
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<li>Custom alphabet support
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<ul>
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<li>A majority of the programs in the MEME Suite now support
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custom alphabets including MEME, DREME, MEME-ChIP, CentriMo,
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SpaMo, AME, FIMO, MAST and Tomtom.</li>
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<li>RNA has been added to the list of built-in alphabets.</li>
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</ul>
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</li>
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<li>Priors for sequence databases
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<ul>
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<li>The FIMO and MCAST web services now have support for position
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specific priors for some selected databases.</li>
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</ul>
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</li>
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<li>SpaMo
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<ul>
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<li>Sensitivity is improved by combining the counts for secondary motif sites in each
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of the four possible orientations in 9 ways corresponding to patterns
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expected when the primary and/or secondary motif is palindromic.</li>
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<li>Sensitivity is improved by using all secondary motif sites scoring above the score threshold
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in the analysis rather than just the best-scoring site. The old SpaMo approach
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can still be used by specifying the new "-usebestsec" switch.</li>
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<li>False positives are reduced because, by default, all occurrences
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of the primary motif are "erased" (other than the central one).
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This reduces the tendency of motifs similar to the primary
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motif to appear enriched. The -keepprimary switch can be used
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to override this behavior so that spacings between multiple
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occurrences of the primary motif can be observed.</li>
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<li>The sequence identifiers for the sequences with the significant spacing
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are now displayed to allow further downstream analysis (e.g., GO or pathway analysis).</li>
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<li>The actual secondary sites are combined into an "inferred motif" and displayed
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as a sequence logo in order to
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make clearer what the putative sites look like. This allows cases where
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the significant secondary motif in the database is similar, but not the same,
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as the motif actually present in the sequences.</li>
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<li>The inferred motif is displayed as a frequency matrix to allow further
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downstream analysis (e.g., using Tomtom to search other motif databases
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to identify motifs more similar to the inferred motif.</li>
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<li>Alignments of the sequences with the significant spacing are displayed as
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sequence logos. Among other purposes, this can allow cases where the
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sequence similarity extends beyond or between the primary and secondary sites,
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suggesting either 1) the regions are repetitive or 2) the actual secondary
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or primary motif sites are distinct from the respective primary and secondary
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motifs used in the analysis.</li>
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<li>The elimination of overly similar sequences has been sped up using a
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heuristic optimization. A bug was also eliminated that caused the
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comparison to involve only the given strands of DNA sequences rather
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than both strands.</li>
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<li>By default, all sequences containing ambiguous characters in the margins
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around the primary motif are now removed. This is necessary for the
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new heuristic similarity search. It also helps insure that the
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uniformity assumption of random motif occurrences since sites with
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ambiguous characters are not scored. This check is turned off when
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the similarity search is disabled using the "-shared" switch.</li>
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<li>A tab-delimitted text output file "spamo.txt" is now created for
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easy parsing by other programs.</li>
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<li>The new -text switch causes SpaMo to create <b>only</b> the text
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file "spamo.txt", skipping the creation of the HTML output file.</li>
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<li>Changed handling of duplicate sequence IDs from 'die' to 'skip'.</li>
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</ul>
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</li>
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<li>fasta-shuffle-letters
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<ul>
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<li>Added capacity to perform efficient, higher-order
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shuffling of FASTA sequences.</li>
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</ul>
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</li>
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</ul>
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</li>
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<li><b>Bug fixes</b>
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<ul>
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<li>taipale2meme
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<ul>
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<li>Changed naming of multiple motifs for
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same TF to start with _1 (rather than no _).</li>
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<li>Fixed bug that was giving motifs duplicate
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names when _2 was reached.</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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<hr>
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<p>
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<b>MEME version 4.10.2 -- Aug 11, 2015</b>
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</p>
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<ul>
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<li><b>New Features and Enhancements</b>
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<ul>
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<li>General
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<ul>
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<li>
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Added the utility script <code>fasta-grep</code>
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for finding matches to a Perl regular expression
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in a FASTA file.
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</li>
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<li>Replaced use of system pseudo-random number generator
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with an implementation of Mersenne Twister, providing
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more consistent results across platforms</li>
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</ul>
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</li>
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<li>File conversion utlities
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<ul>
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<li>Added <code>-seed_start</code>, <code>-seed_end</code>
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and <code>-other_count</code> options to rna2meme</li>
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</ul>
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</li>
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<li>FIMO
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<ul>
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<li>Eliminated dependency on XSLT for output</li>
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</ul>
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</li>
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<li>MCAST
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<ul>
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<li>Added support for Position Specific Priors (PSP)</li>
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<li>Improved modeling of p-value distribution: GC content added as a
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parameter in EM estimation of exponential distribution.</li>
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<li>Eliminated dependency on XSLT for output.</li>
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</ul>
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<li>Web pages
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<ul>
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<li>Added a job submission rate limiter to the web server</li>
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<li>Added additional check to all job submission forms to ensure
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the combined form input size is smaller than 80MB
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</li>
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<li>Added links for viewing the load on the alternative servers</li>
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<li>Improvements to the display of sequence and motif databases</li>
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</ul>
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</li>
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<li>sequence-update database utility
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<ul>
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<li>Numerous enhancements and fixes</li>
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</ul>
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</li>
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</ul></li>
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<li><b>Bug fixes</b>
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<ul>
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<li>Documentation
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<ul>
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<li>Numerous documentation fixes and improvements</li>
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</ul>
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</li>
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<li>General
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<ul>
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<li>Added check for sequences shorter than the motif
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used to scan them</li>
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<li>
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Fixed the parsing of MEME motif files to handle cases when the
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E-values are written out in different formats
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</li>
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<li>Fixed the writing of MEME motif files so the
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E-values are written out using the same formatting in (hopefully) all circumstances
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</li>
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</ul>
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</li>
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<li>Web pages
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<ul>
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<li>Fixed the logic used to display server news and notices
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to take into account differences between the clock of the server
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and the local computer's clock. </li>
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<li>Fixed a bug where the webserver was not logging
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the job submission times </li>
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<li>Fixed a bug in the website FASTA file validator
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which was incorrectly rejecting sequence weights for being out of range</li>
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<li>Added more obvious links to the motif database
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overview page from the job submission pages</li>
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<li>Changed download page to prevent caching of the inner frame
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in the Safari web browser</li>
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<li>Fixed handling of non-ASCII input on all web-forms</li>
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<li>Fixed a server error caused by the absence of cookies.</li>
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<li>Made disallowed alphabets for sequence inputs on web forms
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more obvious by using a red cross-out over the names
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</li>
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<li>Fixed inclusion of example files for GLAM2 and minimal
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MEME motifs for the website install
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</li>
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<li>
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Improved the error message the MEME reports
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when given a single sequence without using "any number of repeats" (ANR) mode
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</li>
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<li>Fixed incorrect URL in RSAT downloader configuration
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</li>
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</ul>
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</li>
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<li>AME
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<ul>
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<li>Fixed bug causing segfault</li>
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<li>
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Fixed bug causing the maximum motif width to be incorrect
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resulting in a dependency on motif order
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</li>
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<li>Fixed failure to generate log files</li>
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</ul>
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</li>
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<li>GLAM2
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<ul>
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<li>
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Fixed generation of sequence logos for GLAM2 motifs with pure deletion columns
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</li>
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</ul>
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</li>
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<li>MAST
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<ul>
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<li>MAST now ignores WEIGHTS section in FASTA files</li>
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</ul>
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</li>
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<li>Tomtom
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<ul>
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<li>
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Fixed submission to Tomtom from GLAM2 DNA output
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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<hr>
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<p>
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<b>MEME version 4.10.1 -- Mar 19, 2015</b>
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</p>
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<ul>
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<li><b>New Features and Enhancements</b>
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<ul>
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<li>Improved Web Pages
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<ul>
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<li>Updated the schematic on the home page and added more "hover" blurbs
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explaining what tools and databases do.</li>
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<li>Created separate man pages for the Web and Command Line versions
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of all commands.</li>
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<li>Use same blurb for blurb, web man page and command line man page for each tool.</li>
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<li>Added links to Manual on each tool input form (top right).</li>
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<li>Email address are not required for job submissions.</li>
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</ul>
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</li>
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<li>Improved test scripts
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<ul>
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<li>Updated the testing scripts to work with Automake's
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custom test driver specification.</li>
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<li>Split the tests into a file per program to make maintaince
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easier.</li>
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</ul>
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</li>
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<li>CentriMo
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<ul>
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<li>Added "Region Position" sort to allowing sorting from left to right.</li>
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<li>Renamed "Region Center" sort to "Region Distance".</li>
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</ul>
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</li>
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<li>FIMO
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<ul>
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<li>Improved the XML to HTML stylesheet.</li>
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</ul>
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</li>
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<li>MCAST
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<ul>
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<li>Improved the XML to HTML stylesheet.</li>
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</ul>
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</li>
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<li>SpaMo
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<ul>
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<li>The elimination of overly similar sequences has been sped up using a
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|
heuristic optimization.</li>
|
|
<li>By default, all sequences containing ambiguous characters in the margins
|
|
around the primary motif are now removed. This is necessary for the
|
|
new heuristic similarity search. It also helps insure that the
|
|
uniformity assumption of random motif occurrences since sites with
|
|
ambiguous characters are not scored. This check is turned off when
|
|
the similarity search is disabled using the "-shared" switch.
|
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</li>
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</ul>
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</li>
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<li>getsize
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<ul>
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<li>Added capacity to perform efficient, higher-order
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shuffling of FASTA sequences.</li>
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</ul>
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</li>
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<li>update-sequence-db
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<ul>
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<li>Added extra configuration file options for updater URLs so
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in theory local mirrors can be used.</li>
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</ul>
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</li>
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<li>transfac2meme
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<li>beeml2meme
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<ul>
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<li>Added ability to use the "NA" line as
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the ID and make the consensus letter in
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matrix lines optional in order to support
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TRANSFAC-like formats (i.e., Swiss Regulon).
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</li>
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</ul>
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<ul>
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<li>Added ability to process multiple files.</li>
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<li>Added ability to draw alternate ID and URL from a snapshot
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of a specific Uniprobe webpage.</li>
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</ul>
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</li>
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<li>iupac2meme
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<ul>
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<li>Added ability to invert the meaning of a symbol group with '^'.
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For example with a DNA motif [A] would match A but [^A] would
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match C, G, or T.</li>
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</ul>
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</li>
|
|
<li>taipale2meme
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|
<ul>
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<li>Changed naming of multiple motifs for
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same TF to start with _1 (rather than no _).</li>
|
|
<li>Fixed bug that was giving motifs duplicate
|
|
names when _2 was reached.</li>
|
|
</ul>
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|
</li>
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<li>README
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<ul>
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<li>Reformatted the README as Markdown styled text.</li>
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</ul>
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</li>
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</ul>
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</li>
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<li><b>Bug fixes</b>
|
|
<ul>
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<li>Webpages
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<ul>
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<li>Fixed various issues with viewing the website and outputs
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in Internet Explorer.</li>
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</ul>
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|
</li>
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<li>Sequence uploads
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<ul>
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<li>RNA sequences are now converted to DNA again as was the
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behaviour in release 4.9.1. This is a temporary fix to avoid
|
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problems in MEME and AME where 'U's were not supported. Support
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for custom alphabets is intended for a future release.</li>
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</ul>
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</li>
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<li>CentriMo
|
|
<ul>
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<li>Ensure rounding up on window sites for the text output.
|
|
The text output was using bankers rounding which occasionally
|
|
caused different results to the rounding displayed in the HTML
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output.</li>
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</ul>
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</li>
|
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<li>FIMO
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|
<ul>
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<li>Fixed PSP reader to honor --parse-genomic-coord option.</li>
|
|
<li>Removed unused --max-seq-length option.</li>
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|
<li>Changed FIMO to not attempt to rewind the file when reading
|
|
from standard input. FIMO will now report an error when you
|
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attempt to scan more than one motif when reading the sequences
|
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from standard input because handing multiple motifs requires
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rewinding the file with FIMO's current architecture.</li>
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</ul>
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</li>
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<li>MEME
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<ul>
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<li>Fixed bug when PSP files contain zeros; 1e-16 is now added to those entries.</li>
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</ul>
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|
</li>
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<li>MCAST
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<ul>
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<li>Fixed bugs in purging of low score matches when max stored matched reached.</li>
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<li>Fixed GC ranging and match purging code.</li>
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</ul>
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</li>
|
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<li>SpaMo
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<ul>
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<li>A bug was eliminated that caused the sequence similarity
|
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comparison to involve only the given strands of DNA sequences
|
|
rather than both strands.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.10.0 -- May 6, 2014</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>Website
|
|
<ul>
|
|
<li>The side-bar menu was completely rewritten to work in all the
|
|
documentation even when the MEME Suite has not been installed.</li>
|
|
<li>Many confusing, extraneous and hard to update summary pages
|
|
that the old side-bar menu required have been removed.</li>
|
|
<li>All the command-line documentation has been standardised to
|
|
a common pattern which will hopefully make it easier to understand.</li>
|
|
<li>The job submission logic has been rewritten using Java
|
|
Servlets instead of Perl CGI scripts. This should enable better
|
|
integration with Opal as the Perl interface to Opal had not been
|
|
updated with the more recent Opal versions.</li>
|
|
<li>The job submission pages use new techniques to validate
|
|
files before you click the submit button.</li>
|
|
<li>All the pages that accept MEME formatted motifs can accept
|
|
hand typed motifs using IUPAC codes, lists of sites or
|
|
frequency/count matrices.</li>
|
|
|
|
</ul>
|
|
</li>
|
|
<li>MEME
|
|
<ul>
|
|
<li>Removed the shell script that used to be needed to execute serial ('meme.bin') or
|
|
parallel ('meme_p') versions of MEME. MEME is now a single executable ('meme') like
|
|
the other C-based MEME Suite programs.</li>
|
|
<li>New HTML output with a more compact overview, delayed
|
|
loading to handle display of larger sequence counts and a
|
|
combined motif site/scan diagram.</li>
|
|
</ul>
|
|
</li>
|
|
<li>CentriMo
|
|
<ul>
|
|
<li>New feature in output to plot site probability vs. distance from center of sequence.</li>
|
|
</ul>
|
|
</li>
|
|
<li>MEME-ChIP
|
|
<ul>
|
|
<li>Print value of <code>-filter-thresh</code> in header of MOTIFS section of output.</li>
|
|
</ul>
|
|
</li>
|
|
<li>AME
|
|
<ul>
|
|
<li>Added web interface to the AME "Analysis of Motif Enrichment" tool.
|
|
AME reports (known) motifs that are enriched in your input nucleotide sequences
|
|
compared with either (a) shuffled versions of your sequences or (b)
|
|
control sequences that you supply.</li>
|
|
<li>Correct Fisher's Exact test to be one-tailed rather than two-tailed so
|
|
that under-represented motifs don't get small p-values.
|
|
<li>Disable "better" ranksum test mode (it's broken).
|
|
</ul>
|
|
</li>
|
|
<li>rna2meme
|
|
<ul>
|
|
<li>Allow reading from standard input if input filename is '-'.</li>
|
|
</ul>
|
|
</li>
|
|
<li>Sequence Databases
|
|
<ul>
|
|
<li>Added more sophisticated tool for server operators to
|
|
download sequence databases.</li>
|
|
<li>Added UCSC Mammal Genome sequence databases.</li>
|
|
<li>Sequence databases are now versioned where possible and timestamped where not.
|
|
You can select the desired version for search via MAST, FIMO, MCAST or GLAM2SCAN.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.9.1 -- August 23, 2013</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>AME
|
|
<ul>
|
|
<li>Make "overwrite directory ame_out" default behavior like other MEME Suite programs.</li>
|
|
<li>Change test on --pvalue-report-threshold from "<" to "≤".</li>
|
|
<li>Add help popups for Split, p-value and Corrected p-value.</li>
|
|
</ul>
|
|
</li>
|
|
<li>CentriMo
|
|
<ul>
|
|
<li>Added the ability to scan with the reverse complement
|
|
of each motif separately (--sep). This is useful when
|
|
the sequences have strand information (e.g., TSSs) and the
|
|
motif has a prefered orientation.</li>
|
|
<li>Added the ability to limit the minimum size of regions
|
|
whose significance is computed (--minreg). This allows
|
|
the user to restrict regions to a width range so that the
|
|
significance levels of all motifs can be compared for
|
|
regions of the same size.
|
|
</li>
|
|
<li>Added the ability to zoom-in on a section of the output graph.</li>
|
|
</ul>
|
|
</li>
|
|
<li>DREME
|
|
<ul>
|
|
<li>Add "Time" to end of text output file.</li>
|
|
</ul>
|
|
</li>
|
|
<li>MCAST
|
|
<ul>
|
|
<li>Move "display more" arrow in HTML output to left (same as MAST output).</li>
|
|
</ul>
|
|
</li>
|
|
<li>MEME-ChIP
|
|
<ul>
|
|
<li>Documented the -group-thresh and -group-weak switches; changed
|
|
default -group-weak threshold to be only 2 times (not 10 times)
|
|
the -group-thresh to avoid excessive merging of motif clusters.
|
|
</li>
|
|
<li>The number of motifs to be found by MEME or DREME may
|
|
now be set to zero on the command line
|
|
to prevent either of the programs from being
|
|
run. CentriMo and the motif clustering algorithm will still
|
|
be run, allowing MEME-ChIP to be used as a front-end to CentriMo.
|
|
</li>
|
|
<li>Add -centrimo-flip option so that matches on reverse strand
|
|
will be reflected around center of sequence. This permits
|
|
(non-palindromic) motifs with asymmetric binding to be detected.</li>
|
|
<li>Added -meme-maxsize option to expose MEME's maxsize option.</li>
|
|
</ul>
|
|
</li>
|
|
<li>SpaMo
|
|
<ul>
|
|
<li>The (slow) sequence redundancy step can now be skipped
|
|
by setting the --shared option to zero.</li>
|
|
<li>Added extra documentation recommending the use of a
|
|
repeat-masker before running SpaMo.</li>
|
|
</ul>
|
|
</li>
|
|
<li>Other
|
|
<ul>
|
|
<li>The utility fasta-get-markov is now implemented in c
|
|
and is much faster than before. It is backwards compatible
|
|
with the Perl implementation but now has some new features
|
|
like the ability to specify input and output files,
|
|
a progress display and summary of the sequence
|
|
counts/sizes like from getsize.</li>
|
|
<li>Implemented a better hashing function for use by the
|
|
hash table datastructure which should improve performance
|
|
and also fix an overflow bug that was present in the
|
|
old function.</li>
|
|
<li>Script fasta-fetch now handles sources with genomic coordinates that list negative strands.</li>
|
|
<li>Disabled building of obsolete programs and made an effort to remove unused "fossil" code.</li>
|
|
<li>Enforced separation of library and program code so Python and Perl libraries
|
|
should no longer be installed into the bin directory.</li>
|
|
<li>Added a link to the MEME Suite's Google Scholar page from the citing page.</li>
|
|
<li>Improved resiliency of get_db_csv to poorly behaved FTP servers.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Bug fixes</b>
|
|
<ul>
|
|
<li>AME
|
|
<ul>
|
|
<li>Fixed usage message to include defaults.</li>
|
|
<li>Fix bug in computation of corrected p-value (LOGEV).</li>
|
|
<li>Fixed a bug where short sequences combined being scanned
|
|
with long motifs could cause the program to attempting
|
|
scanning before the sequence start and into unallocated
|
|
memory.</li>
|
|
</ul>
|
|
</li>
|
|
<li>CentriMo
|
|
<ul>
|
|
<li>Fixed bug causing log-odds scores of "N" columns to be non-zero in CentriMo.</li>
|
|
<li>Increased accuracy of log-odds scores in CentriMo by upping PSSM_RANGE.</li>
|
|
<li>Fixed off by 0.5 error in output graph where the graph was shifted right by half a unit.
|
|
This error wasn't noticeable until we added the zooming feature.</li>
|
|
<li>Now only creates links to motifs that have URLs.</li>
|
|
</ul>
|
|
</li>
|
|
<li>DREME
|
|
<ul>
|
|
<li>Fixed a bug where DREME would crash when it couldn't find Ghostscript.</li>
|
|
</ul>
|
|
</li>
|
|
<li>FIMO
|
|
<ul>
|
|
<li>Fixed bug where FASTA sequence IDs were truncated at ":" if they looked like BED format.</li>
|
|
<li>Fixed bug with all "N" motifs causing crash.</li>
|
|
<li>Fixed bug causing log-odds scores of "N" columns to be non-zero in FIMO.</li>
|
|
<li>Fixed bug causing free of unallocated memory.</li>
|
|
<li>Fixed bug where the release date would be truncated in output.</li>
|
|
<li>Increased accuracy of log-odds scores in FIMO by upping PSSM_RANGE.</li>
|
|
</ul>
|
|
</li>
|
|
<li>MAST
|
|
<ul>
|
|
<li>Fixed the output's display of the background model when the sequence composition was used.</li>
|
|
<li>Corrected a link to an example motif file on the job submission form.</li>
|
|
</ul>
|
|
</li>
|
|
<li>MCAST
|
|
<ul>
|
|
<li>Fix MCAST bug: wasn't printing motif match threshold.</li>
|
|
</ul>
|
|
</li>
|
|
<li>MEME
|
|
<ul>
|
|
<li>Fixed memory link and double free when <code>-cons</code> option was used.</li>
|
|
</ul>
|
|
</li>
|
|
<li>MEME-ChIP
|
|
<ul>
|
|
<li>Fixed a bug where a motif could be discovered by MEME but excluded by MEME-ChIP due to a large E-value
|
|
and then be rediscovered by CentriMo by being centrally enriched. This sequence of events would cause the
|
|
output to break as the Javascript made assumptions that were incorrect.</li>
|
|
<li>Fixed a bug where on some Perl installations the timeout would not be caught and handled correctly.</li>
|
|
</ul>
|
|
</li>
|
|
<li>SpaMo
|
|
<ul>
|
|
<li>Corrected a link to an example motif file on the job submission form.</li>
|
|
</ul>
|
|
</li>
|
|
<li>Tomtom
|
|
<ul>
|
|
<li>Fixed bug in Tomtom's pearson_scores(): replaced integer division with floating point.</li>
|
|
</ul>
|
|
</li>
|
|
<li>Other
|
|
<ul>
|
|
<li>When sequences are skipped due to a duplicate name the warning message is not generic anymore.</li>
|
|
<li>Replaced broken link to old user forum with link to new Q&A site.</li>
|
|
<li>Removed non-functional -P switch from ceqlogo. Use "-d ''" to supress fineprint. </li>
|
|
<li>Added documentation of "--uniform--" keyword for "--bgfile" switch.</li>
|
|
<li>Updated source for Eukaryotic Promoter Database (listed in etc/db_general.csv).</li>
|
|
<li>Fixed a bug where the release date was being truncated by some older programs in the MEME Suite.</li>
|
|
<li>Fixed usage message of create-priors.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.9.0 patch 4 -- January 18, 2013</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>CentriMo
|
|
<ul>
|
|
|
|
<li>Added computation of <i>p-</i>value ratio whenever
|
|
negative sequences are given. The <i>p-</i>value ratio
|
|
seems to be more useful than the discriminative
|
|
<i>p-</i>value computed in the <code>--disc</code> mode,
|
|
and is much faster to compute. Motifs are now sorted by
|
|
<i>p-</i>value ratio by default when negative sequences
|
|
are given and <code>--disc</code> is not.</li>
|
|
|
|
<li>Added feature to supress plotting of negative sequence
|
|
enrichment curves so a single run can be used for
|
|
comparative and absolute enrichment analysis.
|
|
|
|
<li>Sorting on Region Center now sorts by increasing
|
|
absolute value (centrality) of the location of the region.</li>
|
|
|
|
<li>The "region" sorting feature menu is now locked to the
|
|
same value as the "motifs" feature menu, unless a checkbox
|
|
is checked. This helps prevent confusion.</li>
|
|
|
|
|
|
<li>Improved documentation popups.</li>
|
|
|
|
<li>Fixed bug in the Fisher's Exact test (affected AME,
|
|
too).</li>
|
|
|
|
<li>Added new standalone utility: fisher_exact</li>
|
|
|
|
</ul>
|
|
</li>
|
|
<li>MEME-ChIP
|
|
<ul>
|
|
<li>Added -centrimo-local switch to allow CentriMo to perform
|
|
local motif enrichment as part of MEME-ChIP.</li>
|
|
</ul>
|
|
<li>FIMO
|
|
<ul>
|
|
<li>Added <code>--parse-genomic-coords</code> option.
|
|
This option turns on parsing of UCSC style genomic
|
|
coordinates from sequence headers.</li>
|
|
</ul>
|
|
</li>
|
|
<li>taipale2meme
|
|
<ul>
|
|
<li>Add options [-nc <c>]+ and [-oc <c>] to accomodate
|
|
format of Jolma2013 Cell paper.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<b>Bug fixes</b>
|
|
<ul>
|
|
<li>Fixed buffer overflow bug in shift_sequence().</li>
|
|
|
|
<li>Fixed bug in DREME: -norc option resulted in incorrect PSSM.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.9.0 -- October 2, 2012</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>CentriMo
|
|
<ul>
|
|
<li>Added local mode for detecting uncentered enriched
|
|
regions.</li>
|
|
<li>Added discriminative mode which takes two datasets
|
|
and uses the Fisher's exact test to detect discriminatively
|
|
enriched regions.</li>
|
|
<li>Added listing of sequence IDs in output for best
|
|
enriched regions.</li>
|
|
<li>Added score threshold optimization mode.</li>
|
|
<li>Updated website form to give access to local mode and
|
|
discriminative mode.</li>
|
|
</ul>
|
|
</li>
|
|
<li>FIMO
|
|
<ul>
|
|
<li>Simplified command line options controlling output threshold.</li>
|
|
<li>FIMO no longer emits a wiggle format file.
|
|
The wiggle file contained the same information as the GFF file,
|
|
but was more verbose.
|
|
</li>
|
|
<li>Output of '--text' option now matches format of 'fimo.txt' file.</li>
|
|
<li>Text file now provides explicit strand information.</li>
|
|
<li>Text file now lists start and stop coordinates in increasing order relative to the positive strand
|
|
for all matches.</li>
|
|
<li>HTML output is now limited to the 1000 most significant matches.</li>
|
|
</ul>
|
|
</li>
|
|
<li>MEME-ChIP
|
|
<ul>
|
|
<li>Complete rewrite of the MEME-ChIP program to run MEME,
|
|
DREME, Tomtom and CentriMo.</li>
|
|
<li>New output which collates all the motifs found by the
|
|
called programs with links to their outputs.</li>
|
|
<li>New website form allows choice of motif database and
|
|
adds more options for DREME and CentriMo.</li>
|
|
</ul>
|
|
</li>
|
|
<li>TOMTOM
|
|
<ul>
|
|
<li>Creation of EPS and PNG Logo files is now optional to
|
|
save disk space.
|
|
Two new switches (-png and -eps) have been added to the
|
|
command line version of TOMTOM.</li>
|
|
</ul>
|
|
</li>
|
|
<li>meme-rename
|
|
<ul>
|
|
<li>Added new script meme-rename for mass renaming of
|
|
output html files so they can inhabit the same directory.</li>
|
|
</ul>
|
|
</li>
|
|
<li>psp-gen
|
|
<ul>
|
|
<li>Added handling of ambiguous IUPAC alphabet
|
|
symbols for DNA bases.</li>
|
|
</ul>
|
|
</li>
|
|
<li>New Motif Databases
|
|
<ul>
|
|
<li>Malaria transcription factor motifs from PBM experiments
|
|
(Campbell et al., 2010 PLos Pathogens)</li>
|
|
<li>New motifs derived from the original UniPROBE PBM data using
|
|
a different algorithm (Zhao and Stormo,
|
|
2011 Nature Biotechnology)</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<b>Bug fixes</b>
|
|
<ul>
|
|
<li>Fixed FIMO bug--nucleotide motifs were labeled as polypeptide motifs in GFF output</li>
|
|
<li>Fixed FIMO bug--both motifs and RC motifs were printing in list of best possible matches</li>
|
|
<li>Fixed CentriMo bug--"--motif" option was not functional.
|
|
<li>Fixed bug in gendb--was failing with higher-order models.
|
|
<li>Fixed bug in gendb--was failing with higher-order models.
|
|
<li>Updated the MEME installation guide</li>
|
|
<li>Removed unused documents</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.8.1 -- February 6, 2012</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li><code>CentriMo</code>
|
|
<ul>
|
|
<li>Added method to create custom Encapsulated Postscript
|
|
files of the motif probability graph.</li>
|
|
</ul>
|
|
</li>
|
|
<li><code>MEME-ChIP</code>
|
|
<ul>
|
|
<li>Added SpaMo to the list of programs that MEME-ChIP
|
|
runs.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Bug fixes</b>
|
|
<ul>
|
|
<li>Fixed a typo which was breaking the "Upload your own
|
|
database" feature on Tomtom.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.8.0 -- January 16, 2012</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li><code>CentriMo</code>
|
|
<ul>
|
|
<li> Added HTML output with lots of interactive features
|
|
allowing selecting, sorting and filtering of which motifs to
|
|
display and plot the site-probability curves for.</li>
|
|
<li>Added <code>CentriMo</code> web submission form.</li>
|
|
<li><code>CentriMo</code> now runs as part of <code>MEME-ChIP</code>.</li>
|
|
<li>Can now use motif matches to the given strand only if the
|
|
<code>-norc</code> switch is given. Useful with RNA sequences.</li>
|
|
<li>Removed <code>centrimo-plots</code> program as the new
|
|
HTML output replaces and improves on its purpose.</li>
|
|
</ul>
|
|
</li>
|
|
<li><code>DREME</code>
|
|
<ul>
|
|
<li>Can now look for motifs on the given strand only if the
|
|
<code>-norc</code> switch is given. This can be useful with
|
|
RNA sequences.</li>
|
|
<li>Using given strand only now available as an option on the web
|
|
submission form.</li>
|
|
</ul>
|
|
</li>
|
|
<li><code>MCAST</code>
|
|
<ul>
|
|
<li>Added support for scanning genome scale sequences.</li>
|
|
<li>Added q-values for match scores.</li>
|
|
<li>Revised HTML output to include block diagrams of matches.</li>
|
|
</ul>
|
|
</li>
|
|
<li><code>SpaMo</code>
|
|
<ul>
|
|
<li>SpaMo now normalizes the p-values reported for particular
|
|
motif spacings (bins) only for the number of spacings (bins)
|
|
tested. Previously, SpaMo reported p-values normalized for
|
|
both the number of spacings and the number of motifs tested.</li>
|
|
<li>SpaMo now prints E-values for secondary motifs, which is the
|
|
lowest p-value of any spacing (bin) times the number of secondary
|
|
motifs.</li>
|
|
<li>Added -evalue switch to specify largest E-value allowed for
|
|
secondary motifs.</li>
|
|
</ul>
|
|
</li>
|
|
<li>Other
|
|
<ul>
|
|
<li>Improved memory efficiency for reading FASTA sequences in sequence.py.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Bug fixes</b>
|
|
<ul>
|
|
<li>Fixed segmentation fault in FIMO when option
|
|
<code>--bgfile motif-file</code> is used.</li>
|
|
<li>Fixed png generation code for custom motif logos.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.7.0 -- September 22, 2011</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>DREME can be accessed as a webservice directly which
|
|
allows use of the discriminative motif discovery.</li>
|
|
<li>DREME now produces XML and HTML outputs as well as text.
|
|
These new outputs are accepted where MEME motifs are
|
|
accepted.</li>
|
|
<li>New command-line program
|
|
<a href="centrimo.html">CentriMo</a> and the associated
|
|
<a href="centrimo-plots.html">CentriMo Plots</a> for
|
|
determining which motifs are centrally enriched in ChIP-seq
|
|
output.</li>
|
|
<li>Completely rewrote motif loading code. The main user
|
|
visible difference is that the minimal MEME format is a
|
|
lot more forgiving of spacing and MAST can now accept the
|
|
minimal MEME format without any PSSM section.</li>
|
|
<li>Output fromm all tools nows lists prefered citation.</li>
|
|
<li>Updated and re-formated list of publications.</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Bug fixes</b>
|
|
<ul>
|
|
<li>Occasionally MEME would produce HTML files which could not
|
|
be used as a motif input to other programs. The new motif
|
|
parser should be able to read these files and hence fix this
|
|
problem.</li>
|
|
<li>SpaMo background is now calculated from the sequences as
|
|
stated in the paper.</li>
|
|
<li>The website menu used to use the full URL which
|
|
unfortunately resulted in people bookmarking specific versions
|
|
of the MEME suite rather than the URL for the latest version.
|
|
The website menu has been corrected to use only relative
|
|
URLs.</li>
|
|
<li>Links should now be created to the error messages when
|
|
a webservice fails. This used to work but some setting changed
|
|
the way redirects are buffered.</li>
|
|
<li>Added compiler/linker directives to set stack size for
|
|
Cygwin to 9MB. Cygwin defaults to a 2MB stack, which is too
|
|
small.</li>
|
|
<li>MAST was not handling the <code>-remcorr</code> switch.
|
|
When a motif was removed because it was too correlated, the
|
|
indices of the other motifs could be incorrect. Fixed.</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Known issues</b>
|
|
<ul>
|
|
<li>DREME does not yet support single strand scanning. It is
|
|
planned but wasn't ready for this release.</li>
|
|
<li>Uploading extremely large sequence sets to MEME-ChIP can
|
|
cause a HTTP timeout and/or failure of the CGI script.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.6.1 -- March 21, 2011</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>
|
|
<code>MEME-ChIP</code> command line tool --<br />
|
|
MEME-ChIP was released in 4.6.0 as a web service but it did not
|
|
have a command line equalivent. The webservice has been rewritten
|
|
as a command line tool.
|
|
</li>
|
|
<li>
|
|
<code>TOMTOM</code> -- <br />
|
|
The default TOMTOM scoring algorithm now considers all columns in the
|
|
query motif, not just the aligned columns. This reduces the
|
|
number of spurious alignments including uninformative columns.
|
|
The older scoring system is available via the
|
|
<code>-incomplete-scores</code> option.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Bug fixes</b>
|
|
<ul>
|
|
<li>
|
|
<code>MEME-ChIP</code> --<br />
|
|
<ul>
|
|
<li>
|
|
MEME-ChIP has been rewritten to avoid infinite loops that
|
|
could occur when the webservice was passed parameters including
|
|
colons.
|
|
</li>
|
|
<li>
|
|
The webservice now updates its output with the
|
|
completion of each sub-program so if it is teminated by Opal
|
|
for running too long the already completed output is still avaliable.
|
|
</li>
|
|
<li>
|
|
Error reporting has been improved with the result that
|
|
MEME-ChIP should not be able to fail mysteriously as it has
|
|
on occasion been doing.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
FIMO
|
|
<ul>
|
|
<li>
|
|
The <code>--norc</code> option was being ignored.
|
|
This has been fixed.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
Motiph
|
|
<ul>
|
|
<li>
|
|
The <code>--seed</code> option has been added to set the
|
|
seed for the random number generator.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Known issues</b>
|
|
<ul>
|
|
<li>MEME-ChIP when given very large sequence sets will not complete before the Opal webservice time limit.</li>
|
|
<li>Uploading extremely large sequence sets to MEME-ChIP can cause a HTTP timeout and/or failure of the CGI script.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.6.0 -- December 24, 2010</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>
|
|
<code>MEME-ChIP</code> web service --<br />
|
|
<ul>
|
|
<li><b>Motif Analysis of Large DNA Datasets</b><br />
|
|
The MEME-ChIP service allows submission of a FASTA file of DNA sequences
|
|
of unlimited size and with minimal parameter settings (only the traditional
|
|
MEME web form settings) and runs it through a variety of motif finding and
|
|
analysis tools.
|
|
</li>
|
|
<li>
|
|
<code>dreme</code> --<br />
|
|
added <code>dreme</code> and integrated it into the MEME-ChIP into web service.
|
|
</li>
|
|
<li>
|
|
<code>AME</code> --<br />
|
|
added <code>ame</code> and integrated it into the MEME-ChIP into web service. This
|
|
is a cut-down version of the <code>ame</code> previously described, only supporting one mode
|
|
of motif enrichment analysis.
|
|
</li>
|
|
<li>
|
|
<code>fasta-dinucleotide-shuffle</code> --<br />
|
|
added <code>scripts/fasta-dinucleotide-shuffle</code> and integrated it into the MEME-ChIP into web service.
|
|
Thanks to Peter Clote for allowing use of his dinucleotide shuffle code.
|
|
</li>
|
|
<li>
|
|
<code>fasta-center</code> --<br />
|
|
added <code>fasta-center</code> and integrated it into the MEME-ChIP into web service.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<code>SpaMo</code> beta release --<br />
|
|
The web interface and documentation is currently rather limited but in the interests of
|
|
getting this out for review this is a preview edition of the <b>Spaced Motif analysis tool</b>.
|
|
</li>
|
|
<li>
|
|
<code>FIMO</code> -- <br />
|
|
The <code>FIMO</code> HTML output now explicitly labels the strand,
|
|
rather than indicating the reverse strand by having <cdoe>start</cdoe>
|
|
> than <code>stop</code>.
|
|
The HTML output also now includes the matched sequence.
|
|
The GFF output is now GFF 3.
|
|
</li>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<p>
|
|
<b>MEME version 4.5.0 -- September 6, 2010</b>
|
|
</p>
|
|
<ul>
|
|
<li><b>New Features and Enhancements</b>
|
|
<ul>
|
|
<li>
|
|
<code>Tomtom</code> --<br />
|
|
<ul>
|
|
<li><b>Search multiple databases</b><br />
|
|
Tomtom can now search more than one motif database.
|
|
To keep the ability to have web links for each motif
|
|
they were moved into the MEME motif format itself.
|
|
See the <a href="tomtom.html">documentation</a>.
|
|
</li>
|
|
<li><b>Improvements in submission form</b><br />
|
|
Tomtom's submission form has many new enhancements.
|
|
Motifs can now be specified in 3 formats: IUPAC motifs,
|
|
frequency matrices, and MEME format files.
|
|
Go <a href="../cgi-bin/tomtom.cgi">try it</a>.
|
|
</li>
|
|
<li><b>Improvements in output format</b><br />
|
|
Tomtom now outputs an XML file which it converts into
|
|
the HTML output. The HTML output can dynamically
|
|
draw the motif logos when the images aren't available
|
|
on web browsers supporting HTML5. Additional improvements
|
|
include a summary table at the top giving direct links to the
|
|
top 20 matches for each motif. See the
|
|
<a href="examples/tomtom_example_output_files/tomtom.html">sample</a>.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li><code>FIMO</code> --<br />
|
|
The output for FIMO now includes a
|
|
<a href="https://cgwb.nci.nih.gov/goldenPath/help/wiggle.html">wiggle track format file</a>.
|
|
</li>
|
|
<li>MEME file format --<br />
|
|
The MEME file format now includes an optional URL for each motif. This is used
|
|
to create the links in the Tomtom output. All the XXXX2meme scripts have been
|
|
retrofitted to take this URL parameter.
|
|
</li>
|
|
<li>
|
|
<code>ama-qvalues</code> --<br />
|
|
New script. See the <a href="ama-qvalues.html">documentation</a>.
|
|
</li>
|
|
<li>
|
|
<code>fasta-subsample</code> --<br />
|
|
New script for extracting a random sampling of the sequences
|
|
in a FASTA file. This is especially useful for ChIP-seq
|
|
peak datasets to be input to MEME. Using this script, a
|
|
FASTA file containing a subset of the ChIP-seq peak sequences
|
|
(or any other FASTA file) can be created. The total
|
|
number of sequences should be less than 1000 (preferably less
|
|
than 500), and the total sequence length should be less
|
|
than a few hundred thousand. MEME typically takes about 20 minutes
|
|
per motif with files of 100,000 characters (DNA, both strands, ZOOPS model),
|
|
and scales quadratically in the total sequence length (so a file of
|
|
200,000 characters will take four times as long.)
|
|
This new script can also output the remaining sequences (in a seperate
|
|
file) for use in cross-validation. See the <a href="fasta-subsample.html">documentation</a>.
|
|
</li>
|
|
<li>
|
|
<code>meme2meme</code> --<br />
|
|
New script. See the <a href="meme2meme.html">documentation</a>.
|
|
</li>
|
|
<li>
|
|
<code>rna2meme</code> --<br />
|
|
New script. See the <a href="rna2meme.html">documentation</a>.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.4.0 -- April 23, 2010</b>
|
|
</p>
|
|
<ul>
|
|
<li><b> New Features and Enhancements </b>
|
|
<ul>
|
|
<li>
|
|
<code>MCAST</code> --<br />
|
|
<a href="mcast.html?man_type=web">MCAST</a>
|
|
now been integrated into the MEME Suite web applications.
|
|
MCAST is a tool for searching for
|
|
statistically significant clusters of motifs in DNA sequences.
|
|
MCAST was previously supported on a separate web site.
|
|
</li>
|
|
<li>
|
|
<code>MEME</code><br />
|
|
<ul>
|
|
<li><b> Discriminative motif discovery </b> <br />
|
|
The MEME web server now supports discriminative
|
|
motif discovery. The user may now provide a set
|
|
of "negative sequences" in addition to the normal
|
|
"positive sequences", and MEME will look for
|
|
motifs that are overrepresented in the positive sequences
|
|
relative to the negative sequences.
|
|
</li>
|
|
<li><b> Improvements in output format </b> <br />
|
|
MEME's html output (<a href="examples/meme_example_output_files/meme.html">sample</a>) has been reorganised to
|
|
make important information more accessible as well as to make it aesthetically pleasing. Some of the improvements
|
|
include:<br />
|
|
<ul>
|
|
<li>
|
|
A preview of the motifs found, including their reverse complement for DNA, in miniature at the top of the page.
|
|
</li>
|
|
<li>
|
|
Ability to view full sized reverse-complemented DNA logos.
|
|
</li>
|
|
<li>
|
|
Highlighting of all output for a sequence with a single click.
|
|
</li>
|
|
<li>
|
|
New block diagrams that graphically show the strength (and DNA strand) of motifs,
|
|
and that scale with the size of the browser window.
|
|
</li>
|
|
<li>
|
|
Support for the new web standard HTML5. This allows the motif logos to be viewed without the images
|
|
on supporting web browsers (Firefox, Chrome, Safari). Unfortunately Opera has inadequate text support for canvas
|
|
(the new HTML5 element required for this feat) and Internet Explorer currently doesn't support canvas at all.
|
|
It is anticipated that Internet Explorer 9 will support this feature.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<code>MAST</code> --<br />
|
|
<ul>
|
|
<li><b> Improvements in output format </b> <br />
|
|
</li>
|
|
MAST's html output (<a href="examples/mast_example_output_files/mast.html">sample</a>) has been reorganised to
|
|
make important information more accessible as well as to make it aesthetically pleasing. Some of the improvements
|
|
include:<br />
|
|
<ul>
|
|
<li>
|
|
Everything is now in one place - no longer do you have to search to find the associated annotated sequence for that
|
|
high scoring sequence, as with one click the hidden information is displayed directly below. Additionally if DNA
|
|
strands are scored separately then the sequence only appears in the list once based on the better scoring strand.
|
|
</li>
|
|
<li>
|
|
New block diagrams - incorporating all the improvements in the new MEME block diagrams such as graphical display of
|
|
motif strength, scaling with the browser window and the DNA strand. As an added bonus separately scored strands
|
|
are visible on the same diagram.
|
|
</li>
|
|
<li>
|
|
Interactive annotated sequence - a new range selector allows you to view the sequence around the motif hits of your
|
|
choice, directly relatable to the block diagram. For separate DNA strand scoring only one strand is visible at a time.
|
|
</li>
|
|
<li>
|
|
Now in colour - the annotated sequence for motif hits now have letters colour coded using the same colour scheme
|
|
as MEME motifs.
|
|
</li>
|
|
</ul>
|
|
<li> MAST now outputs xml in a similar fashion to MEME. This has resulted in differences to how you would invoke MAST
|
|
from the <a href="mast.html">command line</a>. Additionally it no longer has the script wrapper.
|
|
</li>
|
|
<li>MAST now uses an xml style sheet to create its html output.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<code>mast2txt</code> --<br />
|
|
Created program <a href="mast2txt.html">mast2txt</a> for outputting the old text format for MAST. Note that there are some
|
|
problems with backwards compatibility in separate scoring mode. The use of the text format is no longer recommended.
|
|
</li>
|
|
<li>
|
|
<code>psp-gen</code> --<br />
|
|
added <code>psp-gen</code> and integrated PSP generation into web service.
|
|
</li>
|
|
<li>
|
|
<code>MHMM</code> --<br />
|
|
Fixed bug in <code>--order</code> option.
|
|
The option was handling motifs with strand identifiers incorrectly.
|
|
</li>
|
|
<li><code>TOMTOM</code> -- <br />
|
|
Added <code>-no-ssc</code> switch to fix problem with
|
|
motifs with few sites having empty logos; this switch is now
|
|
the default for the TOMTOM website.</li>
|
|
<li><code>GOMO</code> --<br />
|
|
Improved gomo html format.
|
|
Added highlighting of the most specific GO terms in
|
|
the html output. This is activated by the switch --dag
|
|
which expects a GO DAG file.</li>
|
|
<li><code>gomo_highlight</code> --<br />
|
|
Added a program to post process gomo xml files to
|
|
identify the go terms which are implied by other
|
|
more specific go terms to allow the specific terms
|
|
to be highlighted in the html output. This is used
|
|
by gomo when the --dag switch is specified.
|
|
</li>
|
|
<li>
|
|
<code>obo2dag</code> --<br />
|
|
Added a tool for generating a GO DAG file from a
|
|
Gene Ontology OBO file.
|
|
</li>
|
|
<li>
|
|
<code>GO DAG format</code> --<br />
|
|
Documented the new GO DAG file format and improved GOMO
|
|
documentation as well as the command line overview.
|
|
</li>
|
|
<li>
|
|
<code>GLAM2</code> -- <br />
|
|
The output now prints a regular expression in addition to the logo
|
|
for each motif found.
|
|
</li>
|
|
<li>
|
|
<code>MEME motif format</code> --<br />
|
|
Fixed errors in motif format description
|
|
<code>doc/meme-format.html</code> and example files.
|
|
</li>
|
|
<li>
|
|
<code>meme-io</code> --<br />
|
|
Updated meme-io to accept the new MEME html format.
|
|
</li>
|
|
</ul>
|
|
</ul>
|
|
|
|
<hr />
|
|
<p>
|
|
<b>MEME version 4.3.0 -- September 26, 2009</b>
|
|
</p>
|
|
<ul>
|
|
<li>GOMO --
|
|
<br />
|
|
Added comparative genomics to GOMO. GOMO can now use
|
|
multiple, comparative genomes in making its predictions.
|
|
This substantially increases the sensitivity of predictions of roles
|
|
for DNA binding motifs. The GOMO web-service now
|
|
uses GC-compensated AMA <i>p</i>-values.
|
|
<li>AMA --
|
|
<br />
|
|
<i>P</i>-values are no longer printed by default. A switch
|
|
has been added to cause them to be printed.
|
|
<br />
|
|
AMA can now compute GC-content compensated <i>p</i>-values.
|
|
The GC-content of an individual sequence is used in estimating
|
|
the <i>p</i>-value of its AMA score.
|
|
</ul>
|
|
|
|
<hr />
|
|
|
|
<p>
|
|
<b>MEME version 4.2.0 -- June 22, 2009</b>
|
|
</p>
|
|
<ul>
|
|
<li> MEME --
|
|
<br />
|
|
MEME now can use position-specific priors (PSP) to improve
|
|
motif discovery. The PSP is specified using the
|
|
<code>-psp pspfile</code> switch to MEME.
|
|
<li>GOMO --
|
|
<br />
|
|
Added the ability to choose either maximum or average
|
|
binding affinity as the scoring function.
|
|
<br />
|
|
Fixed a bug--was using
|
|
maximum affinity by default, contrary to the documentation.
|
|
<li>AMA --
|
|
<br />
|
|
AMA now computes <i>p</i>-value of each sequence based on
|
|
a 0-order background model for the dataset.
|
|
<br />
|
|
Improved speed and memory efficiency; was re-reading sequences
|
|
and storing them in memory.
|
|
<br />
|
|
Fixed bug--was using max-odds by default
|
|
and the --scoring switch was being ignored.
|
|
<li>MAST -- website now supports protein databases even when
|
|
DNA database contains long sequences.
|
|
<li>Installation --
|
|
<br />
|
|
Now all programs in the MEME suite are built.
|
|
The --enable-both configure switch is now obsolete.
|
|
<br />
|
|
Simplified the build process by removing support for separately building
|
|
the tools formerly included in Meta-MEME.
|
|
<br />
|
|
Update on-line documentation.
|
|
<br />
|
|
Simplified "quick install" instructions are provided in <code>INSTALL</code>
|
|
and in <code>doc/meme-install.html</code>.
|
|
</ul>
|
|
|
|
<hr />
|
|
|
|
<p>
|
|
<b>MEME version 4.1.1</b>
|
|
</p>
|
|
<ul>
|
|
<li>Improved documentation.</li>
|
|
<li>Increased default number of iterations for GLAM2.</li>
|
|
<li>Improved error handling for sequence data.</li>
|
|
<li>Added links to server activity summary.</li>
|
|
<li>Fixed bug in install process when <code>--enable-both</code> not used.</li>
|
|
</ul>
|
|
|
|
<hr />
|
|
|
|
<p>
|
|
<b>MEME version 4.1.0</b>
|
|
</p>
|
|
|
|
<ul>
|
|
|
|
<li>New tool: GOMO -- Finding Genome Ontology terms associated with
|
|
DNA binding motifs.
|
|
<li>Added FIMO and GOMO buttons to MEME output to make it
|
|
easy to use discovered motifs to search sequence databases
|
|
and to identify the role of DNA binding motifs.
|
|
<li>Fixed placement of sidebar menu in Internet Explorer for output of CGI scripts.</li>
|
|
<li>Fixed support for OpenMPI in MEME.</li>
|
|
<li>Improved the efficiency of FIMO.</li>
|
|
<li>
|
|
Made the <code>-text</code> option to FIMO produce results on-the-fly,
|
|
without sorting or q-values. This mode allows very large databases to
|
|
be searched, without storing intermediate results.</li>
|
|
|
|
<li>
|
|
Modified the command line syntax for <code>gendb</code>, for
|
|
consistency with the rest of the suite.</li>
|
|
|
|
</ul>
|
|
|
|
<hr>
|
|
<p>
|
|
<b>MEME version 4.0.0 -- June 13, 2008</b>
|
|
</p>
|
|
<ul>
|
|
<li><b> New Features and Enhancements </b>
|
|
<ul>
|
|
<li> MEME and Meta-MEME are now integrated as "The MEME Suite".</li>
|
|
<li> New web-based tools:
|
|
<ul>
|
|
<li> GLAM2 and GLAM2SCAN--discovery and scanning of <b>gapped</b> motifs</li>
|
|
<li> Tomtom--comparing motifs</li>
|
|
<li> FIMO--basic motif scanning (complements MAST)</li>
|
|
</ul>
|
|
</li>
|
|
<li> Enhancements of existing tools:
|
|
<ul>
|
|
<li> Sequence LOGOS now enhance MEME output.</li>
|
|
<li> Compare new motifs to databases of motifs
|
|
via Tomtom by clicking an easy-to-use button on MEME and GLAM2
|
|
output.</li>
|
|
<li> Improved local search (branching search) in MEME
|
|
(command line version only).</li>
|
|
<li> Hundreds of new genomic and upstream sequence databases
|
|
are now supported for scanning by MAST, FIMO or GLAM2SCAN.</li>
|
|
<li> Tomtom supports four motif databases: JASPAR, Transfac, SCPD
|
|
and MacIsaac Yeast.</li>
|
|
</ul>
|
|
<li> The MEME Suite tools now have web servers powered by OPAL,
|
|
and return their results via the web, rather than by email.</li>
|
|
<li> A single <a href="../search.html">web server</a> portal simplifies
|
|
different types of motif scanning tasks</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr />
|
|
<p>
|
|
<b>MEME version 3.5.7 -- December 14, 2007</b>
|
|
</p>
|
|
<ul>
|
|
<li><b> New Features and Enhancements </b>
|
|
<ul>
|
|
<li>Parallel MEME is compiled when no scheduler is found but MPICH is detected.</li>
|
|
<li>Opal integration with meme.</li>
|
|
<li>Added --enable-webservice=<path_to_build-opal.xml> configure flag.
|
|
Used to automate deployment of MEME inside an Opal installation as a web service.</li>
|
|
<li>Added --enable-web=<opal_url> configure flag.
|
|
Used to enable building of the MEME web portal.
|
|
A URL for an Opal-exposed MEME web service must be entered.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 3.5.5 -- May 31, 2007</b>
|
|
</p>
|
|
<ul>
|
|
<li><b> New Features and Enhancements </b>
|
|
<ul>
|
|
<li>MAST -hit_list can now handle very long sequences
|
|
and prints ALL hits regardless of the sequence E-value cutoff.
|
|
It splits them into "swaths". The -hit_list switch now
|
|
overrides the -seqp switch, and hits are NOT sorted
|
|
by the E-value of the sequence.</li>
|
|
</ul></li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 3.5.4 -- September 21, 2006 </b>
|
|
</p>
|
|
<ul>
|
|
<li><b> New Features and Enhancements </b>
|
|
<ul>
|
|
<li>Changed the MAST -hit_list behavior to print ONLY a list
|
|
of the non-overlapping significant motif matches in each
|
|
sequence in a machine-readable format.
|
|
(More complete documentation is given in the MAST "usage"
|
|
message. Type "mast" on the UNIX command line to see the usage message.)
|
|
An example of the (complete) output of MAST using the -hit_list switch is:
|
|
<pre>
|
|
# All non-overlapping hits in all sequences.
|
|
# sequence_name motif hit_start hit_end score hit_p-value
|
|
ce1cg -2 8 22 1459.90 1.67e-06
|
|
ara +2 2 16 1661.18 5.04e-08
|
|
bglr1 +2 1 15 1274.97 1.42e-05
|
|
cya -2 19 33 1101.37 6.64e-05
|
|
gale +2 5 19 1076.21 8.11e-05
|
|
ilv -2 6 20 1098.85 6.78e-05
|
|
malk +2 37 51 1085.02 7.56e-05
|
|
ompa +2 5 19 1583.18 2.43e-07
|
|
# mast tests/meme.crp0.oops tests/crp0.s -stdout -hit_list -m 2
|
|
</pre></li>
|
|
<li>New "regular expression" section added to each MEME motif.</li>
|
|
</ul></li>
|
|
<li><b>Bug fixes </b>
|
|
<ul>
|
|
<li>Fixed printing of command name in MAST results.</li>
|
|
<li>Fixed the handling of the "View FASTA", "View RAW" and "View motif summary"
|
|
buttons on the MEME form.</li>
|
|
<li>Improved documentation of the "Motif Summary" section of MEME output.</li>
|
|
<li>Fixed bug that prevented having multiple MEME and MAST servers running on a
|
|
single host by different users. Each server is distinguished by the socket number
|
|
it listens on.</li>
|
|
</ul>
|
|
</li>
|
|
<li><b>Known Issues </b>
|
|
<ul>
|
|
<li>The "MetaMEME" button on the top of MEME results page is still not functional.
|
|
Users are advised to go to the MetaMEME web site and submit manually at this time.
|
|
</li>
|
|
<li>MAST: Uploaded file names containing quotation marks may cause the search to
|
|
fail.</li>
|
|
<li>MAST: Uploaded sequences in DOS/Windows format may cause the search to fail.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
|
|
<p>
|
|
<b>MEME version 3.5.3 -- April 20, 2006</b>
|
|
</p>
|
|
<ul>
|
|
<li><b> New Features and Enhancements </b>
|
|
<ul>
|
|
<li>The capability to search three JASPAR databases of DNA motifs
|
|
for matches to a MEME-discovered motif has been added to the MEME
|
|
output form. Pressing the 'COMPARE PSPM' button on the results
|
|
form of a MEME search of DNA sequences will submit the selected
|
|
motif PSPM to the JASPAR 'Compare' server. This will allow you
|
|
to determine if your motif is similar to any known motifs contained
|
|
in one of the three JASPAR motif databases.</li>
|
|
</ul>
|
|
</li>
|
|
|
|
<li><b>Bug fixes </b>
|
|
<ul>
|
|
<li>The "MAST" button on the top of MEME results page now automatically loads the
|
|
motifs from the MEME results for MAST search. A user only needs to choose the database
|
|
(uploaded or server side) to search against.</li>
|
|
</ul>
|
|
</li>
|
|
|
|
</ul>
|
|
|
|
<hr/>
|
|
|
|
<p>
|
|
<b>MEME version 3.5.2 -- March 1, 2006</b>
|
|
</p>
|
|
<ul>
|
|
<li><b> New Features and Enhancements </b>
|
|
<ul>
|
|
<li>Newly designed web interface using javascript and css styling.</li>
|
|
<li>Add support for Macos X server startup.</li>
|
|
<li>Add meme-install.html with detailed explanation of installation
|
|
procedures.</li>
|
|
</ul>
|
|
</li>
|
|
|
|
<li><b>Bug fixes </b>
|
|
<ul>
|
|
<li>In "configure" remove check dependency on parallel condition when
|
|
creating server executables.</li>
|
|
<li>Path to images/ in cgi scripts.</li>
|
|
<li>Description syntax in linux startup script meme.linux.</li>
|
|
<li>Provide fix for a cygwin's new line representation when searching strings.</li>
|
|
<li>Bug in e_step (oops.c)</li>
|
|
<li>Bug caused by typo "MEME_BINbin"</li>
|
|
<li>Remove use of min() in meme.pl</li>
|
|
<li>Remove obsolete argument sample_prob from subseq7()</li>
|
|
<li>Remove OS-dependent declarations of accept(), bind(), connect(),
|
|
socket(), listen(), htons(). They are defined in system header files.</li>
|
|
</ul>
|
|
</li>
|
|
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 3.5.1 -- December 15, 2005 </b>
|
|
</p>
|
|
<ul>
|
|
<li>
|
|
<b>Bug fixes </b>
|
|
<ul>
|
|
<li>Revert binary and scripts names to what they used to be in version prior to 3.5.0.
|
|
The binary executables have an extension ".bin", and the shell scripts have
|
|
their extension ".csh" removed. This allows to keep compatibility with
|
|
earlier versions.</li>
|
|
<li>Change startup scripts to start servers as a user specified during configuration.
|
|
If none were specified, then the uid of the user who runs configure will be
|
|
used.</li>
|
|
<li>Always install files in etc/. </li>
|
|
<li>Always install Globals.pm in lib/perl/.</li>
|
|
<li>Move meme-explanation.html from web/html/ to etc/. This allows to run scripts that do
|
|
conversion to html when web site is not installed.</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<b>Enhancements</b>
|
|
<ul>
|
|
<li> Added support for Macos X (serial version only, without server)</li>
|
|
<li> Users can now compare DNA motifs to the motifs in the JASPAR database of transcription
|
|
factor binding site motifs. A button is provided in the PSPM section of each DNA motif
|
|
on the MEME output form for this purpose. Clicking on the "Compare PSPM x to known motifs
|
|
in JASPAR database" sends the motif to the JASPAR website, which returns any similar motifs
|
|
that are found.</li>
|
|
<li>Add meme_config.csh file that is used automatically by csh scripts to set
|
|
needed environment variables.</li>
|
|
<li>Move job.out file (created when SGE scheduler is used) to LOGS/</li>
|
|
<li>Add '--with-serial' option to 'configure.ac' for compiling only serial
|
|
version</li>
|
|
<li>Disable installation of web by default. To install use --with-web configure
|
|
option.</li>
|
|
<li>Lower prerequisite version for autoconf to 2.53, and add missing functions in m4/.
|
|
Add check for autoconf version in bootstrap, and use m4 functions when
|
|
needed.</li>
|
|
<li>Change option '--with-mpi' to '--with-mpidir'</li>
|
|
</ul>
|
|
</li>
|
|
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 3.5.0 -- September 15, 2005 </b>
|
|
</p>
|
|
<p>This is the <b>12th year of MEME development</b>. The current anniversary
|
|
maintenance release
|
|
for MEME contains a number of improvements to the installation and configuration of MEME/MAST
|
|
servers and clients. Thanks to Nadya Williams of SDSC/NBCR for this work.
|
|
</p>
|
|
<ul>
|
|
<li>
|
|
<b>Refactoring of installation and configuration</b>
|
|
<ul>
|
|
<li>Restructure source directory tree to ease configuration.</li>
|
|
<li>Highly simplified and optimized installation and configuration for MEME and MAST servers
|
|
and clients using GNU autoconf/automake tools. </li>
|
|
<li>Multiple configuration options available via arguments to "configure".</li>
|
|
<li>Default installation of MEME, MAST server and clients, as well as the web
|
|
site.</li>
|
|
<li>Separate installation of server, client or web site if desired.</li>
|
|
<li>Create a small test suite for 'make test'.</li>
|
|
<li>Implement procedures for standard 'configure', 'make', 'make test', and 'make
|
|
install'.</li>
|
|
<li>Create scripts to run MEME/MAST servers as services, and automatically restarted them
|
|
when physical host server reboots. Currently, Linux and SunOS are supported.</li>
|
|
<li>Simplified start of the servers with 'start-mast' and 'start-meme' scripts.</li>
|
|
<li>Encapsulate site-specific variables in Globals.pm for perl scripts
|
|
and in meme_config for sh scripts.</li>
|
|
<li>Add csh and sh configuration scripts to set working environment.</li>
|
|
<li>Availability as a Rocks Roll for integration with
|
|
<a href="http://www.rocksclusters.org">Rocks based cluster system</a>.</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<b>Enhancements</b>
|
|
<ul>
|
|
<li>Sent MEME/MAST search results via an email as attachments, rather than inlined in the
|
|
message body. This allows the MEME output to be saved properly for subsequent
|
|
use with MetaMEME. It also reduces the chance of the output being modified by email
|
|
filters.</li>
|
|
<li>Check email addresses for entry accuracy using javascript. Thanks to Chris
|
|
Misleh of NBCR for this feature.</li>
|
|
<li>Check email addresses for valid domain names.</li>
|
|
<li>Create new 'runtests' script to run all test suites. Simplify parsing of the
|
|
output.</li>
|
|
<li>Update FAQ(s) for MEME and MAST.</li>
|
|
<li>Separate web-related files by type (html, cgi or image) and create a dir structure
|
|
to support it. This simplifies web maintenance.</li>
|
|
<li>Add examples of database and motif sequences files.</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<b>Known Issues</b>
|
|
<ul>
|
|
|
|
<li>The new meme and mast are binary executables, not shell scripts as they used to be.
|
|
When run with the appropriate arguments, they produce text (non-html) output. To get
|
|
the "old" behavior of meme and mast with the html output, use meme.csh and mast.csh
|
|
(without -text option). The following table gives new vs. old usage comparison.
|
|
<pre>
|
|
old new
|
|
meme myfile -dna -text > meme.res meme myfile -dna > meme.res # output will be a text file
|
|
meme myfile -dna > meme.res meme.csh myfile -dna > meme.res # output will be an html file
|
|
mast meme.res mast.csh meme.res # output will be an html file
|
|
</pre>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
|
|
<li>
|
|
<b>Support Team Members</b>
|
|
Wilfred W. Li, Ph.D., Nadya Williams, M.S., Chris Misleh, and Timothy Bailey, Ph.D.
|
|
</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 3.0.14 -- July, 2005 </b>
|
|
</p>
|
|
<ul>
|
|
<li>
|
|
<b>Bug Fixes</b>
|
|
<ul>
|
|
<li>
|
|
an array out of bound error when MEME is run in parallel mode using certain DNA
|
|
sequences with the "look for palindromes only" option enabled. Thanks to Tim Kaiser of
|
|
SDSC/NBCR for the bug fix.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<b>User Support</b>
|
|
<ul>
|
|
<li>all user questions are directed to our support team meme-suite@uw.edu.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 3.0 -- December, 2000 </b>
|
|
</p>
|
|
|
|
<ul>
|
|
<li>
|
|
<b>MEME enhancements</b>
|
|
<ul>
|
|
<li>
|
|
<b>Hypertext output:</b> MEME now reports its output in hypertext (HTML)
|
|
format with appropriate internal hot links among the results and the
|
|
self-contained documentation on how to interpret them. The
|
|
alignments are color-coded by nucleic acid or amino acid category.
|
|
</li>
|
|
<li>
|
|
<b>Direct MAST search:</b> MEME motifs can now be used to search
|
|
sequence databases using MAST simply by clicking on a button on the
|
|
MEME HTML output document in an HTML-capable email reader or browser.
|
|
</li>
|
|
<li>
|
|
<b>Direct BLOCKS search:</b> MEME motifs can now be submitted to the
|
|
BLOCKS multiple alignment processor by clicking on a button on
|
|
the MEME HTML output document in an HTML-capable email reader or
|
|
browser. This allows MEME motifs to be converted to LOGOS or trees,
|
|
and to be used to search other databases of motifs.
|
|
</li>
|
|
<li>
|
|
<b>New objective function:</b> MEME searches for motifs that optimize
|
|
the statistical significance of the log likelihood ratio of the
|
|
occurrences of the motif.
|
|
</li>
|
|
<li>
|
|
<b>E-values:</b> MEME computes and reports the statistical significance
|
|
of motifs as the E-value of the log likelihood ratio. This provides
|
|
an objective measure of how likely the motif is to be biologically
|
|
significant.
|
|
</li>
|
|
<li>
|
|
<b>E-value stopping criterion:</b> MEME will now stop when a motif
|
|
whose E-value is above a user-given threshold is found. This guarantees
|
|
that only motifs with a given E-value or better will be present in the
|
|
output.
|
|
</li>
|
|
<li>
|
|
<b>Handling reverse complement DNA strands:</b> MEME now handles
|
|
reverse complement DNA strands correctly with all model types:
|
|
OOPS, ZOOPS and TCM.
|
|
</li>
|
|
<li>
|
|
<b>Handling of ambiguous characters:</b> MEME now handles ambiguous
|
|
DNA and protein letters by converting them to the character "X".
|
|
MEME treats the "X" character as "unknown", and correctly computes
|
|
the probabilities of motif occurrences containing it.
|
|
</li>
|
|
<li>
|
|
<b>Higher-order background models:</b> MEME now allows the user to
|
|
specify a Markov model of arbitrary order via a file of tuple
|
|
frequencies. This appears to improve the ability to discriminate
|
|
between biologically interesting DNA motifs and motifs that are
|
|
artifacts of the higher order statistics of DNA sequence.
|
|
</li>
|
|
<li>
|
|
<b>Multiple-alignment-based motif trimming:</b>
|
|
MEME defines a motif as
|
|
a set of subsequences that can be correctly aligned without gaps.
|
|
MEME can now trim
|
|
the edges of motifs based on a local multiple alignment with gaps. MEME
|
|
first determines the occurrences of the motif, then aligns each
|
|
occurrence to the highest-scoring occurrence. These are combined
|
|
into a multiple alignment, and MEME looks for a set of columns with
|
|
no gaps. If a set of gapless columns at least <minw> wide is not
|
|
found, MEME searches for a set with at most 1, 2, ... etc gaps until
|
|
a set is found.
|
|
</li>
|
|
<li>
|
|
<b>Prior distribution on the number of occurrences:</b> MEME now
|
|
places a prior on the number of occurrences that controls how
|
|
strong the bias towards motifs with a given number of sites is.
|
|
Using a prior improves the performance of MEME with DNA, where the
|
|
megaprior heuristic (used by default with protein sequences),
|
|
is not applicable.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
|
|
<li>
|
|
<b>MAST enhancements</b>
|
|
<ul>
|
|
<li>
|
|
<b>Combining DNA strands:</b> MAST now combines the score of a
|
|
site in a DNA sequence with the score of the corresponding site
|
|
on the reverse complement strand. (The final score for the site
|
|
is the maximum of the two scores.)
|
|
</li>
|
|
<li>
|
|
<b>Scoring DNA strands separately:</b> MAST still allows each strand
|
|
of a DNA sequence to be treated as a separate sequence at the
|
|
user's request.</li>
|
|
<li>
|
|
<b>Ignoring reverse complement DNA:</b> MAST also allows the user to
|
|
score only the given DNA strand, not scoring the reverse complement
|
|
strand at all.
|
|
</li>
|
|
<li>
|
|
<b>Background model:</b> MAST now allows the user to specify the
|
|
background residue frequencies used for computing E-values of scores.
|
|
</li>
|
|
<li>
|
|
<b>Composition-adjusted statistics:</b> MAST can now use a different
|
|
random model for each target sequence, based on the letter composition
|
|
of that sequence. This can greatly reduce erroneous matches due
|
|
to biased sequence composition.
|
|
</li>
|
|
<li>
|
|
<b>New databases:</b>
|
|
The MAST website includes several new databases including "upstream"
|
|
sequences for E. coli, B. subtilis and S. cerevesiae, and many complete
|
|
genomes from GenBank.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
|
|
<li>
|
|
<b>MEME and MAST enhancements</b>
|
|
<ul>
|
|
<li>
|
|
<b>MEME and MAST can be installed under the following operating systems:</b>
|
|
<ul>
|
|
<li> Mac OS X</li>
|
|
<li> Linux (various manufacturers)</li>
|
|
<li> SunSparc workstations (SunOS and Solaris operating systems)</li>
|
|
<li> Decalpha workstations (OSF/1 operating system)</li>
|
|
<li> Silicon Graphics workstations (IRIX version 5.3 operating system)</li>
|
|
<li> Intel Paragon parallel computers</li>
|
|
<li> Cray T3D parallel computers</li>
|
|
<li> IBM SP (AIX operating system)</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 2.2 -- February 25, 1998 </b>
|
|
</p>
|
|
<ul>
|
|
<li>
|
|
<b>MEME enhancements</b>
|
|
<ul>
|
|
<li>Sequence weights can be given in the input sequence file.</li>
|
|
<li>
|
|
The sites composing each motif are output in BLOCKS or FASTA format.
|
|
BLOCKS format motifs can be converted to LOGOS, PSSMS and phylogeny trees
|
|
using the <a href="http://blocks.fhcrc.org/blocks/process_blocks.html">
|
|
Blocks Multiple Alignment Processor</a>.
|
|
</li>
|
|
<li>
|
|
A "negative" dataset may be specified causing the motifs to be optimized
|
|
to discriminate between the training set family and the negative family.
|
|
(This option is only available when you install MEME on your own computer.)
|
|
</li>
|
|
<li>
|
|
An advanced version of the MEME data submission form allows
|
|
<ul>
|
|
<li> discovering palindromic DNA motifs,</li>
|
|
<li> discovering motifs occurring on both DNA strands, and</li>
|
|
<li> discovering more than ten motifs.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<b>MAST enhancements</b>
|
|
<ul>
|
|
<li>
|
|
DNA sequences (translated in six reading frames) can be searched
|
|
using protein motifs.
|
|
</li>
|
|
<li>
|
|
<a href="examples/mast_example_output_files/mast.html">Hypertext (HTML) output</a>
|
|
including links to the ENTREZ database and
|
|
improved motif diagrams are now output.
|
|
</li>
|
|
<li>Additional searchable databases added to the MAST website.</li>
|
|
<li>
|
|
The annotation section of output is smaller now since only
|
|
regions in sequences where the motifs are present are printed.
|
|
</li>
|
|
<li>
|
|
The ambiguous characters "*" and "-" are now permitted in motifs
|
|
and sequence databases. They are treated as a single, unknown
|
|
character in databases, and replaced by a weighted average of
|
|
scores in motifs.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 2.1 -- March 25, 1997 </b>
|
|
</p>
|
|
|
|
<ul>
|
|
<li>
|
|
<b>Enhancements</b>
|
|
<ul>
|
|
<li>MAST output now includes measurements of similarities between
|
|
all pairs of motifs in the query and a warning if any motifs
|
|
are too similar. (Too similar motifs in a query can cause
|
|
some p-values and e-values to be underestimated. These motifs
|
|
can be removed from the query and MAST re-run to avoid the problem.)</li>
|
|
<li>Cray T3E parallel computer now supported for MEME and MAST.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 2.0 -- October 17, 1996 </b>
|
|
</p>
|
|
<ul>
|
|
<li>
|
|
<b>Enhancements</b>
|
|
<ul>
|
|
<li>
|
|
The output format of MEME has been
|
|
improved to aid readability and user-friendliness.
|
|
</li>
|
|
<li>
|
|
MEME and MAST have been compiled and tested on:
|
|
<ul>
|
|
<li> SunSparc workstations (SunOS and Solaris operating systems)</li>
|
|
<li> Decalpha workstations (OSF/1 operating system)</li>
|
|
<li> Silicon Graphics workstations (IRIX version 5.3 operating system)</li>
|
|
<li> Intel Paragon parallel computers</li>
|
|
<li> Cray T3D parallel computers </li>
|
|
</ul>
|
|
</li>
|
|
|
|
<li>
|
|
MAST has been completely rewritten to provide more accurate
|
|
p-values and to run significantly faster.
|
|
</li>
|
|
<li>A MAST server has been added to the MEME system website.</li>
|
|
<li>
|
|
The MAST server lets you use the motifs found by MEME in your sequences
|
|
to search a wide variety of sequence databases including:
|
|
<ul>
|
|
<li> nr (non-redundant protein and nucleotide databases)</li>
|
|
<li> month (new or revised sequences in the last 30 days)</li>
|
|
<li>
|
|
swissprot (the last major release of the SWISS-PROT protein sequence
|
|
database)
|
|
</li>
|
|
<li> genpept (protein translations from the GenBank feature table)</li>
|
|
<li> dbest (expressed sequence tag database)</li>
|
|
<li> dbsts (sequence tag site database)</li>
|
|
</ul>
|
|
</li>
|
|
|
|
<li> Several improvements have been made to the MEME website:
|
|
<ul>
|
|
<li>
|
|
You can now give the name of a file containing your sequences
|
|
instead of having to cut-and-paste the sequences themselves.
|
|
</li>
|
|
<li>
|
|
You may ask MEME to favor wide motifs instead of the (default) narrow
|
|
motifs; this is especially useful with small sequence sets (fewer than
|
|
10 sequences.)
|
|
</li>
|
|
<li> The on-line documentation of MEME has been expanded and improved.</li>
|
|
<li>
|
|
MEME now determines the type of your sequences
|
|
(PROTEIN or DNA) automatically.
|
|
</li>
|
|
<li>
|
|
The MEME server now runs MAST on your sequences to make it easy for you
|
|
to see the ordering and spacing of the motifs MEME discovered.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
NOTE and PROBER have been removed from the MEME system since their
|
|
functionality is now superseded by MAST.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 1.4 -- February 29, 1996 </b>
|
|
</p>
|
|
<ul>
|
|
<li>
|
|
Megaprior heuristic added to MEME.
|
|
<ul>
|
|
<li>
|
|
MEME now uses the megaprior heuristic with TCM models and the modified
|
|
megaprior heuristic with ZOOPS models (by default). This greatly improves
|
|
the sensitivity and selectivity of motifs using these types of models.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
P-value computation added to MAST.
|
|
<ul>
|
|
<li>
|
|
MAST now computes p-values for sequences when searching large databases.
|
|
This provides better discrimination between true and false positives than
|
|
using z-scores. MAST is still only available via ftp, not via the web server.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li> Various bug fixes to MEME. </li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 1.3 -- December 18, 1995 </b>
|
|
</p>
|
|
<ul>
|
|
<li>MEME web server introduced!</li>
|
|
<li> Various bug fixes to MEME.</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
<p>
|
|
<b>MEME version 1.2 -- November 27, 1995 </b>
|
|
</p>
|
|
<ul>
|
|
<li> MAST homology searcher introduced!
|
|
<ul>
|
|
<li>
|
|
MAST allows accurate homology searches of databases using motifs generated
|
|
by MEME. The scores from all motifs characterizing a family are combined,
|
|
normalized for sequence length, and sorted by z-score. The output of MAST
|
|
is similar to that of BLAST, but, used in conjunction with MEME, MAST
|
|
allows searching for sequences related to an entire family, not just a
|
|
single sequence in the family. This provides better sensitivity and
|
|
selectivity than single-sequence homology searches.
|
|
MAST is currently only available in the ftp-able code, not via the web server.
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li> Various bug fixes to MEME.</li>
|
|
</ul>
|
|
|
|
<hr/>
|
|
|
|
<p>
|
|
<b>MEME version 1.1 -- June 30, 1995 </b>
|
|
</p>
|
|
<ul>
|
|
<li> Initial release of MEME, NOTE and PROBER.</li>
|
|
</ul>
|
|
<hr />
|
|
<h2>Meta-MEME Release Notes</h2>
|
|
<hr />
|
|
<b>Release 3.3</b>
|
|
<ul>
|
|
<li>
|
|
The program <code>motif-scan</code> has been renamed to
|
|
<a href="fimo.html"><code>fimo</code></a>
|
|
</li>
|
|
</ul>
|
|
<hr />
|
|
<b>Release 3.x, Release 3.3</b>, March 24, 2007</b>
|
|
<ul>
|
|
<li>
|
|
Added new tools:
|
|
<dl>
|
|
<dt>
|
|
<a href="fimo.html">motif-scan</a>
|
|
</dt>
|
|
<dd>
|
|
Scans a database of sequences for the presence of motifs by
|
|
calculating the p-value of the match to the motif at each position
|
|
in the sequences.
|
|
</dd>
|
|
<dt>
|
|
<a href="shadow.html">shadow</a>
|
|
</dt>
|
|
<dd>
|
|
Calculates the log-odds of a multiple alignment for a given phylogentic
|
|
tree and evolutionary model at each position in the alignment.
|
|
</dd>
|
|
<dt>
|
|
<a href="motiph.html">motiph</a>
|
|
</dt>
|
|
<dd>
|
|
Scans a multiple alignment for the presence of motifs by
|
|
by calculating the p-values of motif-width windows in the alignment
|
|
for a given phylogentic tree and evolutionary model.
|
|
</dd>
|
|
<dt>
|
|
<a href="tomtom.html">tom-tom</a>
|
|
</dt>
|
|
<dd>
|
|
Searches target motifs for elements similar to any in a set of query motifs.
|
|
</dd>
|
|
</dl>
|
|
</li>
|
|
<li>
|
|
Added <code>--global</code> option to <code>mhmms</code>.
|
|
This option causes <code>mhmms</code> to score sequences using the best
|
|
match between the model and the entire sequence.
|
|
The default is to score using the best local match within a sequence.
|
|
</li>
|
|
<li>
|
|
Added <code>--maxhits</code> option to <code>mhmms</code>.
|
|
This option sets an absolute limit to the number of hits
|
|
returned by <code>mhmms</code>.
|
|
The default is to return all hits consistent with the
|
|
E-value and p-value thresholds.
|
|
</li>
|
|
<li>
|
|
Fixed error in <code>mhmms</code> that resulted in a sequence being considered
|
|
a hit even if all positions were matched to a spacer state.
|
|
</li>
|
|
<li>
|
|
Fixed error causing segmentation a fault in <code>mhmms</code> when the
|
|
<code>--motif-scoring</code> or <code>--pthresh</code> options were used.
|
|
</li>
|
|
<li>
|
|
Fixed error causing segmentation a fault in <code>mhmm</code> when the
|
|
<code>--order</code> option was used.
|
|
</li>
|
|
</ul>
|
|
<hr />
|
|
<b>Release 3.21, August 3, 2005</b>
|
|
<ul>
|
|
<li>Modified meme-io.c to be able to parse the output from the latest versions of MEME.</li>
|
|
<li>
|
|
Modified the mcast script: removed the -allow-weak-motifs swich, and added the --keep-unused switch
|
|
to the call to mhmm from mcast.
|
|
</li>
|
|
</ul>
|
|
<hr />
|
|
<b>Release 3.2, October 7. 2004</b>
|
|
<ul>
|
|
<li>Reorganized source directory structure and implemented build
|
|
system using autoconf and automake.</li>
|
|
<li>Updated program documentation.</li>
|
|
</ul>
|
|
<hr />
|
|
<b>Release 3.1, February 4, 2004</b>
|
|
<ul>
|
|
<li>Remove the auxiliary program <code>score-n-store</code>.</li>
|
|
<li>Change command-line processing to follow POSIX.2 standard.</li>
|
|
</ul>
|
|
<hr />
|
|
<b>Release 3.0.1, June 2, 2003</b>
|
|
<ul>
|
|
<li>Add documentation for MCAST.</li>
|
|
</ul>
|
|
<hr />
|
|
<b>Release 3.0, May 15, 2003</b>
|
|
<ul>
|
|
<li>Remove <code>mhmmt</code> (EM training program) and
|
|
<code>mhmma</code> (multiple alignment program).</li>
|
|
<li>Add <code>mhmmscan</code> and the <code>mcast</code> wrapper
|
|
program for searching DNA databases for regulatory modules.</li>
|
|
<li>Allow star topology in <code>mhmm</code>.</li>
|
|
</ul>
|
|
<hr />
|
|
</body>
|
|
</html>
|
|
|