244 lines
14 KiB
Plaintext
Executable File
244 lines
14 KiB
Plaintext
Executable File
********************************************************************************
|
|
MEME - Motif discovery tool
|
|
********************************************************************************
|
|
MEME version 4.11.2 (Release date: Mon Oct 24 12:27:06 2016 -0700)
|
|
|
|
For further information on how to interpret these results or to get
|
|
a copy of the MEME software please access http://meme-suite.org .
|
|
|
|
This file may be used as input to the MAST algorithm for searching
|
|
sequence databases for matches to groups of motifs. MAST is available
|
|
for interactive use and downloading at http://meme-suite.org .
|
|
********************************************************************************
|
|
|
|
|
|
********************************************************************************
|
|
REFERENCE
|
|
********************************************************************************
|
|
If you use this program in your research, please cite:
|
|
|
|
Timothy L. Bailey and Charles Elkan,
|
|
"Fitting a mixture model by expectation maximization to discover
|
|
motifs in biopolymers", Proceedings of the Second International
|
|
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
|
|
AAAI Press, Menlo Park, California, 1994.
|
|
********************************************************************************
|
|
|
|
|
|
********************************************************************************
|
|
TRAINING SET
|
|
********************************************************************************
|
|
DATAFILE= /data/project_roots/PlantAI-dev/.tmp_meme_parallel_test.fa
|
|
ALPHABET= ACDEFGHIKLMNPQRSTVWY
|
|
Sequence name Weight Length Sequence name Weight Length
|
|
------------- ------ ------ ------------- ------ ------
|
|
seq1 1.0000 42 seq2 1.0000 42
|
|
seq3 1.0000 42 seq4 1.0000 42
|
|
********************************************************************************
|
|
|
|
********************************************************************************
|
|
COMMAND LINE SUMMARY
|
|
********************************************************************************
|
|
This information can also be useful in the event you wish to report a
|
|
problem with the MEME software.
|
|
|
|
command: meme /data/project_roots/PlantAI-dev/.tmp_meme_parallel_test.fa -mod anr -protein -nmotifs 1 -minw 6 -maxw 12 -oc /data/project_roots/PlantAI-dev/.tmp_meme_parallel_test_out -nostatus
|
|
|
|
model: mod= anr nmotifs= 1 evt= inf
|
|
object function= E-value of product of p-values
|
|
width: minw= 6 maxw= 12
|
|
width: wg= 11 ws= 1 endgaps= yes
|
|
nsites: minsites= 2 maxsites= 20 wnsites= 0.8
|
|
theta: spmap= pam spfuzz= 120
|
|
global: substring= yes branching= no wbranch= no
|
|
em: prior= megap b= 840 maxiter= 50
|
|
distance= 1e-05
|
|
data: n= 168 N= 4 shuffle= -1
|
|
|
|
sample: seed= 0 ctfrac= -1 maxwords= -1
|
|
Dirichlet mixture priors file: prior30.plib
|
|
Letter frequencies in dataset:
|
|
A 0.048 C 0.000 D 0.071 E 0.000 F 0.071 G 0.024 H 0.048 I 0.095 K 0.071
|
|
L 0.048 M 0.024 N 0.024 P 0.024 Q 0.119 R 0.048 S 0.071 T 0.048 V 0.024
|
|
W 0.048 Y 0.095
|
|
Background letter frequencies (from dataset with add-one prior applied):
|
|
A 0.048 C 0.005 D 0.069 E 0.005 F 0.069 G 0.027 H 0.048 I 0.090 K 0.069
|
|
L 0.048 M 0.027 N 0.027 P 0.027 Q 0.112 R 0.048 S 0.069 T 0.048 V 0.027
|
|
W 0.048 Y 0.090
|
|
********************************************************************************
|
|
|
|
|
|
********************************************************************************
|
|
MOTIF 1 MEME width = 11 sites = 12 llr = 251 E-value = 5.1e-031
|
|
********************************************************************************
|
|
--------------------------------------------------------------------------------
|
|
Motif 1 Description
|
|
--------------------------------------------------------------------------------
|
|
Simplified A :::::::::::
|
|
pos.-specific C :::::::::::
|
|
probability D :::3::33:::
|
|
matrix E :::::::::::
|
|
F :::::7::::3
|
|
G :::3:::::::
|
|
H 3::::::::3:
|
|
I :::33::::3:
|
|
K :::::::3:::
|
|
L :::::3:3:::
|
|
M :::::::::::
|
|
N ::::::::::3
|
|
P ::::::3::::
|
|
Q 3:a::::::3:
|
|
R :7:::::::::
|
|
S 3:::3:::3::
|
|
T :3:::::::::
|
|
V ::::::3::::
|
|
W ::::::::7::
|
|
Y ::::3:::::3
|
|
|
|
bits 7.6
|
|
6.8
|
|
6.0
|
|
5.3
|
|
Relative 4.5
|
|
Entropy 3.8 *
|
|
(30.2 bits) 3.0 ** ** *
|
|
2.3 ***********
|
|
1.5 ***********
|
|
0.8 ***********
|
|
0.0 -----------
|
|
|
|
Multilevel HRQDIFDDWHF
|
|
consensus QT GSLPKSIN
|
|
sequence S IY VL QY
|
|
|
|
|
|
--------------------------------------------------------------------------------
|
|
|
|
--------------------------------------------------------------------------------
|
|
Motif 1 sites sorted by position p-value
|
|
--------------------------------------------------------------------------------
|
|
Sequence name Start P-value Site
|
|
------------- ----- --------- -----------
|
|
seq4 31 8.89e-12 RQDILDLWIY HTQGYFPDWQN Y
|
|
seq3 31 8.89e-12 RQDILDLWIY HTQGYFPDWQN Y
|
|
seq2 31 8.89e-12 RQDILDLWIY HTQGYFPDWQN Y
|
|
seq1 31 8.89e-12 RQDILDLWIY HTQGYFPDWQN Y
|
|
seq4 9 5.96e-10 MKTAYIAK QRQISFVKSHF SRQDILDLWI
|
|
seq3 9 5.96e-10 MKTAYIAK QRQISFVKSHF SRQDILDLWI
|
|
seq2 9 5.96e-10 MKTAYIAK QRQISFVKSHF SRQDILDLWI
|
|
seq1 9 5.96e-10 MKTAYIAK QRQISFVKSHF SRQDILDLWI
|
|
seq4 20 7.58e-10 RQISFVKSHF SRQDILDLWIY HTQGYFPDWQ
|
|
seq3 20 7.58e-10 RQISFVKSHF SRQDILDLWIY HTQGYFPDWQ
|
|
seq2 20 7.58e-10 RQISFVKSHF SRQDILDLWIY HTQGYFPDWQ
|
|
seq1 20 7.58e-10 RQISFVKSHF SRQDILDLWIY HTQGYFPDWQ
|
|
--------------------------------------------------------------------------------
|
|
|
|
--------------------------------------------------------------------------------
|
|
Motif 1 block diagrams
|
|
--------------------------------------------------------------------------------
|
|
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
|
|
------------- ---------------- -------------
|
|
seq4 6e-10 8_[1]_[1]_[1]_1
|
|
seq3 6e-10 8_[1]_[1]_[1]_1
|
|
seq2 6e-10 8_[1]_[1]_[1]_1
|
|
seq1 6e-10 8_[1]_[1]_[1]_1
|
|
--------------------------------------------------------------------------------
|
|
|
|
--------------------------------------------------------------------------------
|
|
Motif 1 in BLOCKS format
|
|
--------------------------------------------------------------------------------
|
|
BL MOTIF 1 width=11 seqs=12
|
|
seq4 ( 31) HTQGYFPDWQN 1
|
|
seq3 ( 31) HTQGYFPDWQN 1
|
|
seq2 ( 31) HTQGYFPDWQN 1
|
|
seq1 ( 31) HTQGYFPDWQN 1
|
|
seq4 ( 9) QRQISFVKSHF 1
|
|
seq3 ( 9) QRQISFVKSHF 1
|
|
seq2 ( 9) QRQISFVKSHF 1
|
|
seq1 ( 9) QRQISFVKSHF 1
|
|
seq4 ( 20) SRQDILDLWIY 1
|
|
seq3 ( 20) SRQDILDLWIY 1
|
|
seq2 ( 20) SRQDILDLWIY 1
|
|
seq1 ( 20) SRQDILDLWIY 1
|
|
//
|
|
|
|
--------------------------------------------------------------------------------
|
|
|
|
--------------------------------------------------------------------------------
|
|
Motif 1 position-specific scoring matrix
|
|
--------------------------------------------------------------------------------
|
|
log-odds matrix: alength= 20 w= 11 n= 128 bayes= 4.9542 E= 5.1e-031
|
|
-180 -169 -198 145 -461 -128 258 -507 -175 -328 -368 -28 -278 132 -178 204 -224 -259 -580 -435
|
|
-270 -225 -495 -44 -606 -278 -423 -563 -180 -386 -438 -277 -387 -416 371 -351 265 -323 -650 -597
|
|
-311 -224 -491 112 -576 -354 -237 -540 -405 -298 -296 -274 -332 305 -308 -398 -379 -334 -581 -622
|
|
-205 -170 213 120 -516 349 -370 169 -337 -326 -394 -55 -319 -439 -362 -230 -263 -181 -664 -544
|
|
-226 -115 -510 -107 -170 -281 -334 170 -442 -165 -243 -290 -371 -521 -389 206 -288 -81 -355 178
|
|
-377 -179 -645 -233 319 -450 -500 -241 -597 263 -125 -465 -443 -625 -523 -501 -424 -128 -446 -306
|
|
-171 -152 203 172 -495 -190 -420 -351 -341 -283 -355 -154 361 -428 -358 -256 -265 341 -653 -558
|
|
-212 -220 201 232 -496 -183 -306 -438 211 251 -315 -87 -284 -292 -104 -245 -239 -217 -589 -490
|
|
-269 -221 -585 -253 -436 -293 -549 -658 -599 -457 -542 -412 -435 -680 -533 221 -413 -382 375 -441
|
|
-222 -148 -357 92 -296 -238 256 162 -147 -160 -233 -171 -321 132 -139 -291 -252 -115 -462 -314
|
|
-452 -230 -587 -209 222 -415 -290 -491 -540 -276 -379 346 -456 -571 -449 -468 -457 -302 -299 190
|
|
--------------------------------------------------------------------------------
|
|
|
|
--------------------------------------------------------------------------------
|
|
Motif 1 position-specific probability matrix
|
|
--------------------------------------------------------------------------------
|
|
letter-probability matrix: alength= 20 w= 11 nsites= 12 E= 5.1e-031
|
|
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000
|
|
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000
|
|
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
|
0.000000 0.000000 0.333333 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
|
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.333333
|
|
0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
|
0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000
|
|
0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
|
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000
|
|
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
|
|
0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333
|
|
--------------------------------------------------------------------------------
|
|
|
|
--------------------------------------------------------------------------------
|
|
Motif 1 regular expression
|
|
--------------------------------------------------------------------------------
|
|
[HQS][RT]Q[DGI][ISY][FL][DPV][DKL][WS][HIQ][FNY]
|
|
--------------------------------------------------------------------------------
|
|
|
|
|
|
|
|
|
|
Time 0.02 secs.
|
|
|
|
********************************************************************************
|
|
|
|
|
|
********************************************************************************
|
|
SUMMARY OF MOTIFS
|
|
********************************************************************************
|
|
|
|
--------------------------------------------------------------------------------
|
|
Combined block diagrams: non-overlapping sites with p-value < 0.0001
|
|
--------------------------------------------------------------------------------
|
|
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
|
|
------------- ---------------- -------------
|
|
seq1 2.84e-10 8_[1(5.96e-10)]_[1(7.58e-10)]_\
|
|
[1(8.89e-12)]_1
|
|
seq2 2.84e-10 8_[1(5.96e-10)]_[1(7.58e-10)]_\
|
|
[1(8.89e-12)]_1
|
|
seq3 2.84e-10 8_[1(5.96e-10)]_[1(7.58e-10)]_\
|
|
[1(8.89e-12)]_1
|
|
seq4 2.84e-10 8_[1(5.96e-10)]_[1(7.58e-10)]_\
|
|
[1(8.89e-12)]_1
|
|
--------------------------------------------------------------------------------
|
|
|
|
********************************************************************************
|
|
|
|
|
|
********************************************************************************
|
|
Stopped because requested number of motifs (1) found.
|
|
********************************************************************************
|
|
|
|
CPU: xialab-System-Product-Name
|
|
|
|
********************************************************************************
|