******************************************************************************** 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/toy_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ toy_chr2R_2942930_294295 1.0000 29 toy_chr2R_2943057_294308 1.0000 30 toy_chr2R_2943142_294316 1.0000 23 toy_chr2R_2943224_294325 1.0000 31 toy_chr2R_2943105_294312 1.0000 22 ******************************************************************************** ******************************************************************************** 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/toy_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= 5 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 135 N= 5 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.278 C 0.222 G 0.222 T 0.278 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 = 5 llr = 53 E-value = 3.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :242::a:::6 pos.-specific C a848:a:626: probability G ::2:::::244 matrix T ::::a::46:: bits 2.2 * * 1.9 * *** 1.7 * *** 1.5 * *** Information 1.3 ** **** * content 1.1 ** ***** ** (15.2 bits) 0.9 ** ***** ** 0.6 ** ******** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel CCACTCACTCA consensus ACA TCGG sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------- toy_chr2R_2943224_294325 + 13 1.35e-06 AAATTAATTC CCCCTCACTGG GCACAACT toy_chr2R_2942930_294295 + 5 3.03e-06 TTCT CCACTCATTCG TGTGAAAGTT toy_chr2R_2943105_294312 + 7 4.57e-06 GATTCA CCCCTCACCGA TTCCG toy_chr2R_2943057_294308 + 7 8.86e-06 ATAGAC CAACTCACTCA CGTGGCAAAC toy_chr2R_2943142_294316 + 4 3.77e-05 AAT CCGATCATGCA TTATTACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- toy_chr2R_2943224_294325 1.3e-06 12_[+1]_8 toy_chr2R_2942930_294295 3e-06 4_[+1]_14 toy_chr2R_2943105_294312 4.6e-06 6_[+1]_5 toy_chr2R_2943057_294308 8.9e-06 6_[+1]_13 toy_chr2R_2943142_294316 3.8e-05 3_[+1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=11 seqs=5 toy_chr2R_2943224_294325 ( 13) CCCCTCACTGG 1 toy_chr2R_2942930_294295 ( 5) CCACTCATTCG 1 toy_chr2R_2943105_294312 ( 7) CCCCTCACCGA 1 toy_chr2R_2943057_294308 ( 7) CAACTCACTCA 1 toy_chr2R_2943142_294316 ( 4) CCGATCATGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 85 bayes= 4.26589 E= 3.9e-001 -897 216 -897 -897 -47 184 -897 -897 53 84 -16 -897 -47 184 -897 -897 -897 -897 -897 185 -897 216 -897 -897 185 -897 -897 -897 -897 143 -897 53 -897 -16 -16 111 -897 143 84 -897 111 -897 84 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5 E= 3.9e-001 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.200000 0.200000 0.600000 0.000000 0.600000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[CA][ACG][CA]TCA[CT][TCG][CG][AG] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- toy_chr2R_2942930_294295 1.15e-04 4_[+1(3.03e-06)]_14 toy_chr2R_2943057_294308 3.54e-04 6_[+1(8.86e-06)]_13 toy_chr2R_2943142_294316 9.81e-04 3_[+1(3.77e-05)]_9 toy_chr2R_2943224_294325 5.65e-05 12_[+1(1.35e-06)]_8 toy_chr2R_2943105_294312 1.10e-04 6_[+1(4.57e-06)]_5 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************