******************************************************************************** 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/Med_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Med_chr2L_13905216_13905 1.0000 19 Med_chr2R_5497257_549726 1.0000 13 Med_chr2L_11454544_11454 1.0000 17 Med_chr2L_13904760_13904 1.0000 14 Med_chr2R_5497430_549745 1.0000 29 Med_chr3R_17209435_17209 1.0000 30 Med_chr2R_5497227_549723 1.0000 12 Med_chr2R_5497285_549729 1.0000 15 Med_chr2R_5497470_549748 1.0000 13 Med_chr3R_21070780_21070 1.0000 30 Med_chr3R_17209509_17209 1.0000 22 Med_chr3R_17209380_17209 1.0000 29 Med_chr2L_13905196_13905 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/Med_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= 13 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 263 N= 13 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.213 C 0.287 G 0.287 T 0.213 Background letter frequencies (from dataset with add-one prior applied): A 0.213 C 0.287 G 0.287 T 0.213 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 10 llr = 62 E-value = 8.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::: pos.-specific C 6::a:: probability G 1a2::7 matrix T 3:8:a3 bits 2.2 * 2.0 * 1.8 * ** 1.6 * ** Information 1.3 **** content 1.1 ***** (8.9 bits) 0.9 ***** 0.7 ****** 0.4 ****** 0.2 ****** 0.0 ------ Multilevel CGTCTG consensus T G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ Med_chr2L_13905196_13905 - 6 3.07e-04 TTTCCAATC CGTCTG GGGTT Med_chr2L_13905216_13905 - 4 3.07e-04 GGCTTAGTCG CGTCTG ATG Med_chr3R_21070780_21070 - 8 5.36e-04 GACGCCACGC TGTCTG CGAATTC Med_chr2R_5497430_549745 + 6 5.36e-04 TTTTT TGTCTG ACTGACTGAC Med_chr2R_5497227_549723 + 2 7.65e-04 T CGTCTT GGGAT Med_chr3R_17209435_17209 + 10 7.65e-04 TTACTGTCT CGTCTT TCAATGTCGG Med_chr2L_11454544_11454 + 11 7.65e-04 ATAATGTGCC CGTCTT A Med_chr2R_5497257_549726 - 5 1.35e-03 CTG CGGCTG CATC Med_chr3R_17209509_17209 + 1 1.65e-03 . GGTCTG GAGTCTAGAC Med_chr3R_17209380_17209 - 5 1.96e-03 CGACGGGGCG TGGCTG GTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Med_chr2L_13905196_13905 0.00031 5_[-1]_9 Med_chr2L_13905216_13905 0.00031 3_[-1]_10 Med_chr3R_21070780_21070 0.00054 7_[-1]_17 Med_chr2R_5497430_549745 0.00054 5_[+1]_18 Med_chr2R_5497227_549723 0.00076 1_[+1]_5 Med_chr3R_17209435_17209 0.00076 9_[+1]_15 Med_chr2L_11454544_11454 0.00076 10_[+1]_1 Med_chr2R_5497257_549726 0.0013 4_[-1]_3 Med_chr3R_17209509_17209 0.0017 [+1]_16 Med_chr3R_17209380_17209 0.002 4_[-1]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=10 Med_chr2L_13905196_13905 ( 6) CGTCTG 1 Med_chr2L_13905216_13905 ( 4) CGTCTG 1 Med_chr3R_21070780_21070 ( 8) TGTCTG 1 Med_chr2R_5497430_549745 ( 6) TGTCTG 1 Med_chr2R_5497227_549723 ( 2) CGTCTT 1 Med_chr3R_17209435_17209 ( 10) CGTCTT 1 Med_chr2L_11454544_11454 ( 11) CGTCTT 1 Med_chr2R_5497257_549726 ( 5) CGGCTG 1 Med_chr3R_17209509_17209 ( 1) GGTCTG 1 Med_chr3R_17209380_17209 ( 5) TGGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 198 bayes= 5.75489 E= 8.5e-001 -997 107 -152 49 -997 -997 180 -997 -997 -997 -52 190 -997 180 -997 -997 -997 -997 -997 223 -997 -997 129 49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 10 E= 8.5e-001 0.000000 0.600000 0.100000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.700000 0.300000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]G[TG]CT[GT] -------------------------------------------------------------------------------- Time 0.11 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Med_chr2L_13905216_13905 8.56e-03 19 Med_chr2R_5497257_549726 2.13e-02 13 Med_chr2L_11454544_11454 1.82e-02 17 Med_chr2L_13904760_13904 7.69e-01 14 Med_chr2R_5497430_549745 2.54e-02 29 Med_chr3R_17209435_17209 3.75e-02 30 Med_chr2R_5497227_549723 1.07e-02 12 Med_chr2R_5497285_549729 4.59e-01 15 Med_chr2R_5497470_549748 7.83e-01 13 Med_chr3R_21070780_21070 2.65e-02 30 Med_chr3R_17209509_17209 5.47e-02 22 Med_chr3R_17209380_17209 9.00e-02 29 Med_chr2L_13905196_13905 9.17e-03 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************