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= ьуmeme/meme.fasta
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
up_purT 1.0000 101 up_purA 1.0000 101
up_folD 1.0000 101 up_guaA 1.0000 101
up_purH 1.0000 101 up_purM 1.0000 101
up_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 ьуmeme/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc ьуmeme/ 
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= 7 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 707 N= 7
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.286 C 0.214 G 0.214 T 0.286
Background letter frequencies (from dataset with add-one prior applied):
A 0.286 C 0.214 G 0.214 T 0.286

P N
MOTIF 1 width = 8 sites = 7 llr = 58 E-value = 2.0e+002

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
11.6 (bits)
Relative Entropy
11.9 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
up_folD + 49 2.45e-05 TACTGAAAGC CGCCGTAT GAGATGTTAG
up_purT + 39 2.45e-05 GTCGCTATTT TGCCGTAT ACTGGCGCGC
up_guaA - 89 4.91e-05 TGTG TGGCGTAT TCCAAAAATA
up_purH + 22 7.36e-05 TAGTCTGTAG CGCCCTAT TAATTGATAG
up_purM + 48 1.68e-04 ACATGTAGCT TGACGTAT TACGGGTATA
up_purA - 55 1.68e-04 AAACGGGAAT CGGCCTAT TTTGTCAGAA
up_purC + 43 2.88e-04 CCTCCGGCTA TGCCGGAG GATATTTATT

Motif 1 block diagrams


Name
Lowest
p-value
Motifs
up_folD 2.45e-05

+1
up_purT 2.45e-05

+1
up_guaA 4.91e-05

-1
up_purH 7.36e-05

+1
up_purM 1.68e-04

+1
up_purA 1.68e-04

-1
up_purC 2.88e-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

[TC]G[CG]C[GC]TAT

Time 0.30 secs.

P N
MOTIF 2 width = 13 sites = 7 llr = 73 E-value = 3.9e+002

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
15.2 (bits)
Relative Entropy
15.1 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
up_guaA + 9 1.70e-07 AGTAAGGCA GCAAATAAACGGG TCTCGAAGTC
up_purA - 66 9.84e-07 TCCATCAATT GAAAAAAAACGGG AATCGGCCTA
up_purH + 79 4.97e-06 AACTGCGACT CCAAATCCAAGGG ATAAAACCA
up_purC + 27 9.64e-06 AGGCGCATAT GAAAAACCTCCGG CTATGCCGGA
up_purT + 58 9.64e-06 CTGGCGCGCG TCAAATTAACGTG TAATCTCCCA
up_folD - 85 1.91e-05 TCT CAAAAATCACCAG GTTGCTTAAA
up_purM + 30 2.89e-05 ATTGCGCATA GCCAATGCACATG TAGCTTGACG

Motif 2 block diagrams


Name
Lowest
p-value
Motifs
up_guaA 1.70e-07

+2
up_purA 9.84e-07

-2
up_purH 4.97e-06

+2
up_purC 9.64e-06

+2
up_purT 9.64e-06

+2
up_folD 1.91e-05

-2
up_purM 2.89e-05

+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

[GC][CA]AAA[TA][ACT][CA]AC[GC][GT]G

Time 0.48 secs.

P N
MOTIF 3 width = 8 sites = 6 llr = 51 E-value = 2.1e+003

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
12.0 (bits)
Relative Entropy
12.4 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
up_purC + 17 2.10e-05 AGAGCCTTAT AGGCGCAT ATGAAAAACC
up_purA - 22 2.10e-05 CCGCGCTGTC AGGCGCAT AATGACGATT
up_purM - 21 8.50e-05 TGCATTGGCT ATGCGCAA TCACCCGAAT
up_folD + 5 8.50e-05 AAGGT AAGCGCAA AAATTGTTCA
up_purT + 13 8.50e-05 TTAACATTAC AGACGCAA TCGTTTTCGT
up_purH - 71 1.83e-04 TTGGATTTGG AGTCGCAG TTTTCTTCAT

Motif 3 block diagrams


Name
Lowest
p-value
Motifs
up_purC 2.10e-05

+3
up_purA 2.10e-05

-3
up_purM 8.50e-05

-3
up_folD 8.50e-05

+3
up_purT 8.50e-05

+3
up_purH 1.83e-04

-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

AGGCGCA[AT]

Time 0.63 secs.

P N
SUMMARY OF MOTIFS


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


Name
Combined
p-value

Motifs
up_purT 1.79e-05

+3
+1
+2
up_purA 3.74e-06

-3
-2
up_folD 3.27e-05

+3
+1
-2
up_guaA 2.07e-05

+2
-1
up_purH 5.09e-05

+1
+2
up_purM 2.44e-04

-3
+2
up_purC 4.48e-05

+3
+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: