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
purA 1.0000 101 purL 1.0000 101
folD 1.0000 101 purD 1.0000 101
guaA 1.0000 101 purK 1.0000 101
purM 1.0000 101 purC 1.0000 101

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= 8 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 808 N= 8
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.262 C 0.238 G 0.238 T 0.262
Background letter frequencies (from dataset with add-one prior applied):
A 0.262 C 0.238 G 0.238 T 0.262

P N
MOTIF 1 width = 9 sites = 8 llr = 71 E-value = 6.5e+000

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
12.7 (bits)
Relative Entropy
12.8 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purK + 55 3.60e-06 ACATTAACGC CATGCTGCA ACGCACTTCC
folD - 69 3.60e-06 GCCAGATTTC CATGCTGCA CGTCATAAAA
purM + 91 6.87e-06 GTAATGTTAA CAGGCTGCA T
purL + 40 2.06e-05 AATTGTCTCA CAGGCTGGA TGCTGCATCA
purC - 47 3.94e-05 GACGACACCA CATTCTGCA AATATCATCG
purD + 42 6.65e-05 GGCGCGCCAT CATGCGGGA GCACACTGTG
guaA - 88 1.06e-04 TGCG CACGTTGCA AGGTGTCATT
purA + 39 3.46e-04 CTTAGCTTAT TTAGCTGCA ATGACCTTGG

Motif 1 block diagrams


Name
Lowest
p-value
Motifs
purK 3.60e-06

+1
folD 3.60e-06

-1
purM 6.87e-06

+1
purL 2.06e-05

+1
purC 3.94e-05

-1
purD 6.65e-05

+1
guaA 1.06e-04

-1
purA 3.46e-04

+1
SCALE
| | | | |
1 25 50 75 100

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

CA[TG]GCTG[CG]A

Time 0.39 secs.

P N
MOTIF 2 width = 8 sites = 6 llr = 55 E-value = 5.9e+002

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
13.2 (bits)
Relative Entropy
13.2 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purC - 57 1.37e-05 CCCCGTCGCG ACGACACC ACATTCTGCA
purM - 18 1.37e-05 CTCCCCCAGC ACGACACC ACTGACCTAT
purA - 92 2.89e-05 T ACGACAAC GAATGGGGTT
purL - 69 4.26e-05 GACCTGTCCG ACCACACC ATAGACATCA
guaA + 79 7.28e-05 GCCTATGTGA ATGACACC TTGCAACGTG
purK + 39 1.05e-04 GACGCTTCCC ACAACAAC ATTAACGCCA

Motif 2 block diagrams


Name
Lowest
p-value
Motifs
purC 1.37e-05

-2
purM 1.37e-05

-2
purA 2.89e-05

-2
purL 4.26e-05

-2
guaA 7.28e-05

+2
purK 1.05e-04

+2
SCALE
| | | | |
1 25 50 75 100

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

ACGACA[CA]C

Time 0.62 secs.

P N
MOTIF 3 width = 8 sites = 2 llr = 21 E-value = 1.5e+004

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
15.0 (bits)
Relative Entropy
15.4 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
purM + 56 2.27e-05 TCACGGGGAG GCGGCAGC TTGATCGGAA
purD - 29 2.27e-05 GCATGATGGC GCGCCAGC CAATATCACT

Motif 3 block diagrams


Name
Lowest
p-value
Motifs
purM 2.27e-05

+3
purD 2.27e-05

-3
SCALE
| | | | |
1 25 50 75 100

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

GCG[CG]CAGC

Time 0.83 secs.

P N
SUMMARY OF MOTIFS


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


Name
Combined
p-value

Motifs
purA 1.24e-02

-2
purL 1.42e-03

+1
-2
folD 1.61e-02

-1
purD 2.21e-03

-3
+1
guaA 8.29e-03

+2
purK 6.99e-04

+1
purM 2.56e-06

-2
+3
+1
purC 1.04e-03

-1
-2
SCALE
| | | | |
1 25 50 75 100

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: