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= motiv_ecoli/meme.fasta
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
guaB 1.0000 100 guaA 1.0000 100
purB 1.0000 100 purR 1.0000 100
purL 1.0000 100 purF 1.0000 100
purN 1.0000 100 purA 1.0000 100
purT 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 motiv_ecoli/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc motiv_ecoli/ 
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 0.276 C 0.224 G 0.224 T 0.276
Background letter frequencies (from dataset with add-one prior applied):
A 0.276 C 0.224 G 0.224 T 0.276

P N
MOTIF 1 width = 13 sites = 6 llr = 83 E-value = 3.2e-002

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
20.0 (bits)
Relative Entropy
19.9 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purL + 8 9.31e-08 TTATTTCC ACGCAAACGGTTT CGTCAGCGCA
purA + 78 2.14e-07 ATCCATTTTT AAGCAAACGGTGA TTTTGAAAA
purT + 47 3.79e-07 ATAAAGACAC ACGCAAACGTTTT CGTTTATACT
purR + 40 3.79e-07 AGGTGTGTAA AGGCAAACGTTTA CCTTGCGATT
guaB + 31 4.22e-07 AAAGGGGTAG ATGCAATCGGTTA CGCTCTGTAT
purN + 24 5.64e-07 GCCCTGCTCA ATGCCAACGGTGA AAACGCGTGG

Motif 1 block diagrams


Name
Lowest
p-value
Motifs
purL 9.31e-08

+1
purA 2.14e-07

+1
purT 3.79e-07

+1
purR 3.79e-07

+1
guaB 4.22e-07

+1
purN 5.64e-07

+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

A[CT]GCAAACG[GT]T[TG][AT]

Time 0.51 secs.

P N
MOTIF 2 width = 14 sites = 9 llr = 96 E-value = 1.4e+001

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
15.9 (bits)
Relative Entropy
15.3 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purL + 28 1.12e-07 TTTCGTCAGC GCATCAGATTCTTT ATAATGACGC
purN - 62 3.35e-07 GCGTTGTTCG GAATCAGAGGCTTT GATGATACCG
purF + 5 3.35e-07 TTTTA TCATCAGATGTTTT TTTGATTATC
purB + 21 6.18e-07 GCGGACGTCT GCAACTGATGTTTT CTCGTAATCG
guaB - 5 7.40e-06 ACCCCTTTTT GCAAAAAATGCTTG CTATC
guaA - 64 9.99e-06 CGAGGCAAGT GAAACAGATAATAT AAATCGCCCG
purA + 31 1.24e-05 ATTTTTGAGT GCAAAAAGTGCTGT AACTCTGAAA
purT + 81 3.53e-05 CGCGCGGAAT TAATCAGGGGATAT TCGTT
purR + 9 5.80e-05 CGGCGTACC GCAACACTTTTGTT GTGCGTAAGG

Motif 2 block diagrams


Name
Lowest
p-value
Motifs
purL 1.12e-07

+2
purN 3.35e-07

-2
purF 3.35e-07

+2
purB 6.18e-07

+2
guaB 7.40e-06

-2
guaA 9.99e-06

-2
purA 1.24e-05

+2
purT 3.53e-05

+2
purR 5.80e-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

[GT][CA]A[AT][CA]A[GA][AG][TG][GT][CTA]T[TA]T

Time 0.92 secs.

P N
MOTIF 3 width = 15 sites = 7 llr = 83 E-value = 2.0e+003

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
17.0 (bits)
Relative Entropy
17.2 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purN - 5 8.80e-08 TGGCATTGAG CAGGGCGAGGGCTTT GTCCA
guaB + 82 2.02e-07 ATTAACCACT CTGGTCGAGATATTG CCC
guaA + 49 7.09e-07 CGCCCGACTT CATGTCGGGCGATTT ATATTATCTG
purF - 42 1.51e-06 CACTTACGCT CTGGGCAAGAAACTT GACGAGCTTT
purB - 39 3.86e-06 TTTTGCCTGA GTGGTCAGGCGATTA CGAGAAAACA
purL + 85 4.70e-06 CGAAAGCTTA GAAGACGAGAGACTT
purA + 9 5.83e-06 AAAAACAGA CTGATCGAGGTCATT TTTGAGTGCA

Motif 3 block diagrams


Name
Lowest
p-value
Motifs
purN 8.80e-08

-3
guaB 2.02e-07

+3
guaA 7.09e-07

+3
purF 1.51e-06

-3
purB 3.86e-06

-3
purL 4.70e-06

+3
purA 5.83e-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

[CG][TA]GG[TG]C[GA][AG]G[ACG][GT][AC][TC]TT

Time 1.18 secs.

P N
SUMMARY OF MOTIFS


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


Name
Combined
p-value

Motifs
guaB 1.25e-09

-2
+1
+3
guaA 2.29e-05

+3
-2
purB 6.44e-06

+2
-3
purR 4.95e-05

+2
+1
purL 1.16e-10

+1
+2
+3
purF 2.47e-06

+2
-3
purN 4.23e-11

-3
+1
-2
purA 2.39e-08

+3
+2
+1
purT 1.14e-05

+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: