******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.5.4 (Release date: ) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. 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.nbcr.net. ******************************************************************************** ******************************************************************************** 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= ../data/oreganno_data/processed_data/regulons_for_one_factor/nub_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ nub_chr2R_8405118_840513 1.0000 14 nub_chr2R_8405152_840516 1.0000 18 nub_chr2R_8405041_840505 1.0000 14 nub_chr2R_8405078_840509 1.0000 14 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme ../data/oreganno_data/processed_data/regulons_for_one_factor/nub_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 18 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 4 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 60 N= 4 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.242 G 0.242 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.242 G 0.242 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 4 llr = 31 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :8:3:a5: pos.-specific C :::38::: probability G :::5::3a matrix T a3a:3:3: bits 2.0 * * * * 1.8 * * * * 1.6 * * * * 1.4 * * * * Information 1.2 *** ** * content 1.0 *** ** * (11.3 bits) 0.8 *** ** * 0.6 ****** * 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TATGCAAG consensus T AT G sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- nub_chr2R_8405041_840505 + 2 8.10e-05 T TATACAAG GCCGC nub_chr2R_8405078_840509 + 2 1.14e-04 T TATGTAAG TAACC nub_chr2R_8405152_840516 - 4 1.30e-04 GCCGCAA TATCCAGG CGG nub_chr2R_8405118_840513 + 2 2.43e-04 T TTTGCATG CCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- nub_chr2R_8405041_840505 8.1e-05 1_[+1]_5 nub_chr2R_8405078_840509 0.00011 1_[+1]_5 nub_chr2R_8405152_840516 0.00013 3_[-1]_7 nub_chr2R_8405118_840513 0.00024 1_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=4 nub_chr2R_8405041_840505 ( 2) TATACAAG 1 nub_chr2R_8405078_840509 ( 2) TATGTAAG 1 nub_chr2R_8405152_840516 ( 4) TATCCAGG 1 nub_chr2R_8405118_840513 ( 2) TTTGCATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 32 bayes= 2.80735 E= 1.1e+001 -865 -865 -865 195 154 -865 -865 -4 -865 -865 -865 195 -4 5 104 -865 -865 163 -865 -4 195 -865 -865 -865 95 -865 5 -4 -865 -865 204 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.1e+001 0.000000 0.000000 0.000000 1.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[AT]T[GAC][CT]A[AGT]G -------------------------------------------------------------------------------- Time 0.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- nub_chr2R_8405118_840513 3.40e-03 14 nub_chr2R_8405152_840516 2.85e-03 18 nub_chr2R_8405041_840505 1.13e-03 1_[+1(8.10e-05)]_5 nub_chr2R_8405078_840509 1.60e-03 14 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************