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= ememe/meme.fasta
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
up_purL 1.0000 101 up_purT 1.0000 101
up_purA 1.0000 101 up_folD 1.0000 101
up_guaA 1.0000 101 up_purD 1.0000 101
up_purR 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 ememe/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc ememe/ 
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= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 1010 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.266 C 0.234 G 0.234 T 0.266
Background letter frequencies (from dataset with add-one prior applied):
A 0.266 C 0.234 G 0.234 T 0.266

P N
MOTIF 1 width = 14 sites = 7 llr = 97 E-value = 2.7e-003

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
20.2 (bits)
Relative Entropy
20.0 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
up_purT + 50 8.23e-09 GAAAAGACAT ACGCAAACGTTTTC GTATATACTG
up_purL + 11 1.55e-08 TTTTATTTCT ACGCAAACGGTTTC GTCGGCGCGT
up_purR + 43 9.47e-08 GGGTGTGTGT AGGCAAACGTTTAC CTGGCGTTTC
up_purM - 25 1.53e-07 CTAACAGGGA AAGCAAACGTTTGC GAGCGTGGTC
up_folD + 12 3.82e-07 TGCATCGGAA ACACAAACGTTAAC TGACAGCGAG
up_purA + 79 6.57e-07 ATCCATTTTT AAGCAAACGGTGAT TTTGAAAA
up_purD + 37 2.11e-06 GCCGCTGCCG ACGAACACGGTATT GCGATGATCT

Motif 1 block diagrams


Name
Lowest
p-value
Motifs
up_purT 8.23e-09

+1
up_purL 1.55e-08

+1
up_purR 9.47e-08

+1
up_purM 1.53e-07

-1
up_folD 3.82e-07

+1
up_purA 6.57e-07

+1
up_purD 2.11e-06

+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

A[CA]GCAAACG[TG]T[TA][AT][CT]

Time 0.58 secs.

P N
MOTIF 2 width = 8 sites = 10 llr = 73 E-value = 5.9e+003

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
10.4 (bits)
Relative Entropy
10.5 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
up_purC - 13 1.50e-05 TGTAATTGTG GTGCGAAA TAGCGGTTAA
up_purD + 92 4.32e-05 GCCATTAATG GAGCGAAA C
up_purL - 67 8.28e-05 AAGCTTTGGT GTGCGCAA GGGGGGAAAC
up_guaA - 36 9.45e-05 CACGAAGGTC GGGCGAAG AAAATCAGGA
up_purM + 8 1.83e-04 GATAACCA GGGCGCAG ACCACGCTCG
up_purA + 30 2.12e-04 CGCAGATTGA GTGCAAAA AGTGCTGTAT
up_folD - 91 3.17e-04 CA GAGAGAAG ATTCCATCTG
up_purT - 71 4.18e-04 TTATTTACCT GCGCGCAG TATATACGAA
up_purR + 89 4.91e-04 CGAGGGTCTG GAGTGAAA TGTA
up_purH - 43 7.17e-04 TGAATTTTTC GTGAAAAA CTCAGCTAAC

Motif 2 block diagrams


Name
Lowest
p-value
Motifs
up_purC 1.50e-05

-2
up_purD 4.32e-05

+2
up_purL 8.28e-05

-2
up_guaA 9.45e-05

-2
up_purM 1.83e-04

+2
up_purA 2.12e-04

+2
up_folD 3.17e-04

-2
up_purT 4.18e-04

-2
up_purR 4.91e-04

+2
up_purH 7.17e-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

G[TAG]G[CA][GA][AC]A[AG]

Time 1.06 secs.

P N
MOTIF 3 width = 8 sites = 10 llr = 72 E-value = 3.6e+003

SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
10.1 (bits)
Relative Entropy
10.4 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME STRAND START P-VALUE SITES
up_purH + 2 2.32e-05 GT CGCCGCAA AATGAGAATA
up_purR - 0 9.61e-05 GGTTGCGGCA CGCCGGAA
up_purD - 25 9.61e-05 GTTCGTCGGC AGCGGCAA TCACTTCGTC
up_guaA - 81 1.21e-04 ACGCTTATTC CGAGGCAA GTGAAACAGA
up_purM - 51 1.46e-04 AAGTTAAATT CGGCGCAA TTCTAACAGG
up_purA - 16 2.23e-04 GCACTCAATC TGCGGCAA ATCCGACCAC
up_purT + 16 2.23e-04 TATATTGCAA GGCAGCAA GAAAAGCAAT
up_purC + 53 6.13e-04 CGGCAGGCGT AGCAGGAA ATGAATACTT
up_folD - 1 6.13e-04 TTTGTGTTTC CGATGCAA A
up_purL - 59 6.64e-04 GTGTGCGCAA GGGGGGAA ACGGCCGTCA

Motif 3 block diagrams


Name
Lowest
p-value
Motifs
up_purH 2.32e-05

+3
up_purR 9.61e-05

-3
up_purD 9.61e-05

-3
up_guaA 1.21e-04

-3
up_purM 1.46e-04

-3
up_purA 2.23e-04

-3
up_purT 2.23e-04

+3
up_purC 6.13e-04

+3
up_folD 6.13e-04

-3
up_purL 6.64e-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

[CAG]G[CAG][GCA]G[CG]AA

Time 1.42 secs.

P N
SUMMARY OF MOTIFS


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


Name
Combined
p-value

Motifs
up_purL 1.00e-06

+1
-2
up_purT 9.23e-07

+1
up_purA 2.54e-05

+1
up_folD 5.22e-05

+1
up_guaA 6.24e-03

-2
up_purD 8.49e-06

-3
+1
+2
up_purR 4.50e-06

-3
+1
up_purH 1.03e-02

+3
up_purM 4.25e-06

-1
up_purC 1.26e-02

-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: