Command line Training Set First Motif Summary of Motifs Termination Explanation


Search sequence databases for the best combined matches with these motifs using MAST.
Search sequence databases for all matches with these motifs using FIMO.
Find Genome Ontology terms associated with upstream sequences matching these motifs using GOMO.
Submit these motifs to BLOCKS multiple alignment processor.


MEME - Motif discovery tool

MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu.

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.sdsc.edu.


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= meme/meme.fasta
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
guaB_guaR 1.0000 100 guaA_b2507 1.0000 100
purB_b1131 1.0000 100 purR_b1658 1.0000 100
purL_purI 1.0000 100 purF_b2312 1.0000 100
purN_b2500 1.0000 100 purA_adeK 1.0000 100
purT_b1849 1.0000 100

COMMAND LINE SUMMARY

This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme meme/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc meme/ 
model: mod= zoops nmotifs= 3 evt= inf
object function= E-value of product of p-values
width: minw= 8 maxw= 50 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 2 maxsites= 9 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 900 N= 9
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.274 C 0.226 G 0.226 T 0.274
Background letter frequencies (from dataset with add-one prior applied):
A 0.274 C 0.226 G 0.226 T 0.274

P N
MOTIF 1 width = 9 sites = 8 llr = 79 E-value = 2.2e-002

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
14.1 (bits)
Relative Entropy
14.3 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purA_adeK + 81 3.32e-06 CCATTTTTAA GCAAACGGT GATTTTGAAA
purL_purI - 81 3.32e-06 TTATTTCCAC GCAAACGGT TTCGTCAGCG
purT_b1849 + 50 7.35e-06 AAAGACACAC GCAAACGTT TTCGTTTATA
purR_b1658 + 43 7.35e-06 GTGTGTAAAG GCAAACGTT TACCTTGCGA
purN_b2500 + 27 1.89e-05 CCTGCTCAAT GCCAACGGT GAAAACGCGT
guaB_guaR - 58 2.55e-05 AGGGGTAGAT GCAATCGGT TACGCTCTGT
guaA_b2507 + 76 4.75e-05 AATCAGGAGC CCAGACGGT AGTTCGGGGA
purB_b1131 + 77 5.57e-05 AACATCAGTT GCAGACGTC CGCCGCCGAC

Motif 1 block diagrams


Name
Lowest
p-value
Motifs
purA_adeK 3.32e-06

+1
purL_purI 3.32e-06

-1
purT_b1849 7.35e-06

+1
purR_b1658 7.35e-06

+1
purN_b2500 1.89e-05

+1
guaB_guaR 2.55e-05

-1
guaA_b2507 4.75e-05

+1
purB_b1131 5.57e-05

+1
SCALE
| | | | |
1 25 50 75

Motif 1 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 1 position-specific scoring matrix


Scan sequence databases for the best match in each sequence using MAST.
Motif 1 position-specific probability matrix


Scan sequence databases for all matches with this motif using FIMO.
Compare to known motifs in motif databases using Tomtom.
Find Genome Ontology terms associated with upstream regions matching this motif using GOMO.
Motif 1 regular-expression

GCA[AG]ACG[GT]T

Time 0.52 secs.

P N
MOTIF 2 width = 14 sites = 9 llr = 94 E-value = 6.1e+001

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
15.7 (bits)
Relative Entropy
15.1 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purL_purI + 58 2.13e-07 GCGTCATTAT AAAGAATCTGATGC GCTGACGAAA
purN_b2500 + 63 2.21e-07 CGGTATCATC AAAGCCTCTGATTC CGAACAACGC
purF_b2312 + 81 9.05e-07 GATAATCAAA AAAACATCTGATGA TAAAA
guaB_guaR - 81 1.93e-06 GATAG CAAGCATTTTTTGC AAAAAGGGGT
purB_b1131 + 26 9.45e-06 GTTAAATGAG CAAGAATTTGTTTT GCCTGAGTGG
purA_adeK - 32 1.30e-05 TTTCAGAGTT ACAGCACTTTTTGC ACTCAAAAAT
guaA_b2507 - 22 1.30e-05 CGGGCGATTT ATATTATCTGTTTC ACTTGCCTCG
purT_b1849 - 82 3.68e-05 ACGA ATATCCCCTGATTA ATTCCGCGCG
purR_b1658 + 12 4.99e-05 GGCGTACCGC AACACTTTTGTTGT GCGTAAGGTG

Motif 2 block diagrams


Name
Lowest
p-value
Motifs
purL_purI 2.13e-07

+2
purN_b2500 2.21e-07

+2
purF_b2312 9.05e-07

+2
guaB_guaR 1.93e-06

-2
purB_b1131 9.45e-06

+2
purA_adeK 1.30e-05

-2
guaA_b2507 1.30e-05

-2
purT_b1849 3.68e-05

-2
purR_b1658 4.99e-05

+2
SCALE
| | | | |
1 25 50 75

Motif 2 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 2 position-specific scoring matrix


Scan sequence databases for the best match in each sequence using MAST.
Motif 2 position-specific probability matrix


Scan sequence databases for all matches with this motif using FIMO.
Compare to known motifs in motif databases using Tomtom.
Find Genome Ontology terms associated with upstream regions matching this motif using GOMO.
Motif 2 regular-expression

[AC][AT]A[GAT][CA][AC][TC][CT]T[GT][TA]T[GT][CAT]

Time 0.94 secs.

P N
MOTIF 3 width = 15 sites = 7 llr = 83 E-value = 2.5e+003

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
17.0 (bits)
Relative Entropy
17.1 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purN_b2500 + 6 1.02e-07 GTGGAC AAAGCCCTCGCCCTG CTCAATGCCA
guaB_guaR + 3 1.94e-07 GGG CAATATCTCGACCAG AGTGGTTAAT
guaA_b2507 + 36 6.84e-07 CAGATAATAT AAATCGCCCGACATG AAGTCGGGCG
purF_b2312 - 43 1.59e-06 AAAGCTCGTC AAGTTTCTTGCCCAG AGCGTAAGTG
purB_b1131 - 46 3.44e-06 TGTTTTCTCG TAATCGCCTGACCAC TCAGGCAAAA
purL_purI + 0 5.19e-06 AAGTCTCTCGTCTTC TAAGCTTTCG
purA_adeK - 10 5.87e-06 TGCACTCAAA AATGACCTCGATCAG TCTGTTTTTT

Motif 3 block diagrams


Name
Lowest
p-value
Motifs
purN_b2500 1.02e-07

+3
guaB_guaR 1.94e-07

+3
guaA_b2507 6.84e-07

+3
purF_b2312 1.59e-06

-3
purB_b1131 3.44e-06

-3
purL_purI 5.19e-06

+3
purA_adeK 5.87e-06

-3
SCALE
| | | | |
1 25 50 75

Motif 3 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 3 position-specific scoring matrix


Scan sequence databases for the best match in each sequence using MAST.
Motif 3 position-specific probability matrix


Scan sequence databases for all matches with this motif using FIMO.
Compare to known motifs in motif databases using Tomtom.
Find Genome Ontology terms associated with upstream regions matching this motif using GOMO.
Motif 3 regular-expression

AA[AG][TG][CA][TCG]C[TC][CT]G[AC]CC[AT][GC]

Time 1.21 secs.

P N
SUMMARY OF MOTIFS


Combined block diagrams: non-overlapping sites with p-value < 0.0001


Name
Combined
p-value

Motifs
guaB_guaR 1.61e-08

+3
-1
-2
guaA_b2507 5.05e-07

-2
+3
+1
purB_b1131 1.88e-06

+2
-3
+1
purR_b1658 5.75e-04

+2
+1
purL_purI 6.64e-09

+3
+2
-1
purF_b2312 4.99e-06

-3
+2
purN_b2500 9.06e-10

+3
+1
+2
purA_adeK 3.19e-07

-3
-2
+1
purT_b1849 1.62e-04

+1
-2
SCALE
| | | | |
1 25 50 75

Motif summary in machine readable format.
Stopped because Stopped because nmotifs = 3 reached..



CPU: kodomo.fbb.msu.ru


EXPLANATION OF MEME RESULTS


The MEME results consist of:

MOTIFS

For each motif that it discovers in the training set, MEME prints the following information: