******************************************************************************** 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/ey_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ey_chr2R_2942930_2942958 1.0000 29 ey_chrX_6621205_6621224_ 1.0000 20 ey_chr2R_2943057_2943086 1.0000 30 ey_chrX_6613614_6613627_ 1.0000 14 ey_chr3R_10731653_107316 1.0000 20 ey_chr2R_2943224_2943254 1.0000 31 ey_chr2L_6542972_6542991 1.0000 20 ey_chr2R_3550800_3550819 1.0000 20 ******************************************************************************** ******************************************************************************** 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/ey_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= 25 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= 184 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.223 G 0.223 T 0.277 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.223 G 0.223 T 0.277 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 11 sites = 8 llr = 77 E-value = 3.3e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :a1::a41::: pos.-specific C a:4:9:1:4:: probability G ::3:1:38196 matrix T ::3a::31514 bits 2.2 * 1.9 ** * * 1.7 ** * * 1.5 ** *** * Information 1.3 ** *** * content 1.1 ** *** * ** (13.8 bits) 0.9 ** *** * ** 0.6 ** *** **** 0.4 ** *** **** 0.2 ****** **** 0.0 ----------- Multilevel CACTCAAGTGG consensus G G C T sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------- ey_chr3R_10731653_107316 + 4 1.06e-06 CCG CAGTCAAGTGG AACATA ey_chrX_6613614_6613627_ - 4 2.38e-06 . CACTCAAGTGT TAT ey_chr2R_2943057_2943086 + 12 3.15e-06 TAGACCAACT CACTCACGTGG CAAACTCG ey_chr2L_6542972_6542991 + 4 6.36e-06 GTT CAATCAAGTGG CAGACA ey_chr2R_3550800_3550819 + 4 3.79e-05 ACC CATTCAGGCTG CAAAGA ey_chr2R_2942930_2942958 + 6 4.36e-05 TTCTC CACTCATTCGT GTGAAAGTTA ey_chr2R_2943224_2943254 - 12 6.21e-05 AGTTGTGCC CAGTGAGGGGG AATTAATTTT ey_chrX_6621205_6621224_ + 4 7.11e-05 ACC CATTCATACGT GATGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ey_chr3R_10731653_107316 1.1e-06 3_[+1]_6 ey_chrX_6613614_6613627_ 2.4e-06 3_[-1] ey_chr2R_2943057_2943086 3.1e-06 11_[+1]_8 ey_chr2L_6542972_6542991 6.4e-06 3_[+1]_6 ey_chr2R_3550800_3550819 3.8e-05 3_[+1]_6 ey_chr2R_2942930_2942958 4.4e-05 5_[+1]_13 ey_chr2R_2943224_2943254 6.2e-05 11_[-1]_9 ey_chrX_6621205_6621224_ 7.1e-05 3_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=11 seqs=8 ey_chr3R_10731653_107316 ( 4) CAGTCAAGTGG 1 ey_chrX_6613614_6613627_ ( 4) CACTCAAGTGT 1 ey_chr2R_2943057_2943086 ( 12) CACTCACGTGG 1 ey_chr2L_6542972_6542991 ( 4) CAATCAAGTGG 1 ey_chr2R_3550800_3550819 ( 4) CATTCAGGCTG 1 ey_chr2R_2942930_2942958 ( 6) CACTCATTCGT 1 ey_chr2R_2943224_2943254 ( 12) CAGTGAGGGGG 1 ey_chrX_6621205_6621224_ ( 4) CATTCATACGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 104 bayes= 4.97728 E= 3.3e-007 -965 216 -965 -965 185 -965 -965 -965 -114 75 16 -15 -965 -965 -965 185 -965 197 -84 -965 185 -965 -965 -965 44 -84 16 -15 -114 -965 175 -114 -965 75 -84 85 -965 -965 197 -114 -965 -965 148 44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 8 E= 3.3e-007 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.375000 0.250000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.125000 0.250000 0.250000 0.125000 0.000000 0.750000 0.125000 0.000000 0.375000 0.125000 0.500000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.625000 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[CGT]TCA[AGT]G[TC]G[GT] -------------------------------------------------------------------------------- Time 0.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ey_chr2R_2942930_2942958 1.66e-03 5_[+1(4.36e-05)]_13 ey_chrX_6621205_6621224_ 1.42e-03 3_[+1(7.11e-05)]_6 ey_chr2R_2943057_2943086 1.26e-04 11_[+1(3.15e-06)]_8 ey_chrX_6613614_6613627_ 1.90e-05 3_[-1(2.38e-06)] ey_chr3R_10731653_107316 2.12e-05 3_[+1(1.06e-06)]_6 ey_chr2R_2943224_2943254 2.61e-03 11_[-1(6.21e-05)]_9 ey_chr2L_6542972_6542991 1.27e-04 3_[+1(6.36e-06)]_6 ey_chr2R_3550800_3550819 7.57e-04 3_[+1(3.79e-05)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************