******************************************************************************** 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/pho_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ pho_chr3R_12725663_12725 1.0000 8 pho_chr3R_12589924_12589 1.0000 20 pho_chr3R_12590048_12590 1.0000 19 pho_chr3R_12589801_12589 1.0000 20 pho_chr3R_12589921_12589 1.0000 23 pho_chr3R_12590026_12590 1.0000 17 pho_chr3R_12725704_12725 1.0000 9 pho_chr3R_12590028_12590 1.0000 20 pho_chr3R_12589820_12589 1.0000 20 pho_chr3R_12589777_12589 1.0000 20 pho_chr3R_12589768_12589 1.0000 140 pho_chr3R_12590084_12590 1.0000 16 ******************************************************************************** ******************************************************************************** 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/pho_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= 12 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 332 N= 12 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.208 C 0.292 G 0.292 T 0.208 Background letter frequencies (from dataset with add-one prior applied): A 0.208 C 0.292 G 0.292 T 0.208 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 12 llr = 84 E-value = 1.5e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 9::::: pos.-specific C ::::a4 probability G 1:aa:1 matrix T :a:::5 bits 2.3 * 2.0 * 1.8 ***** 1.6 ***** Information 1.4 ***** content 1.1 ***** (10.1 bits) 0.9 ***** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel ATGGCT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ pho_chr3R_12590084_12590 + 9 2.24e-04 GGGGTTTT ATGGCT CA pho_chr3R_12590028_12590 - 7 2.24e-04 CTGCCGTT ATGGCT TCCGTG pho_chr3R_12590026_12590 + 7 2.24e-04 GCCGTT ATGGCT TCCGT pho_chr3R_12589921_12589 - 7 2.24e-04 GCGCACCATA ATGGCT GCGCCG pho_chr3R_12589924_12589 - 4 2.24e-04 GCGCACCATA ATGGCT GCG pho_chr3R_12725663_12725 + 1 2.24e-04 . ATGGCT GC pho_chr3R_12589768_12589 - 16 5.38e-04 TGCGACTGAG ATGGCC TCATAATCGT pho_chr3R_12589777_12589 - 7 5.38e-04 CGACTGAG ATGGCC TCATAA pho_chr3R_12725704_12725 - 2 5.38e-04 TG ATGGCC G pho_chr3R_12589801_12589 - 7 5.38e-04 CGTTCGTA ATGGCC GTTTTA pho_chr3R_12589820_12589 - 7 8.53e-04 CGACAGTT ATGGCG ACGGAG pho_chr3R_12590048_12590 + 7 1.61e-03 GGGGGC GTGGCC TAGAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- pho_chr3R_12590084_12590 0.00022 8_[+1]_2 pho_chr3R_12590028_12590 0.00022 6_[-1]_8 pho_chr3R_12590026_12590 0.00022 6_[+1]_5 pho_chr3R_12589921_12589 0.00022 6_[-1]_11 pho_chr3R_12589924_12589 0.00022 3_[-1]_11 pho_chr3R_12725663_12725 0.00022 [+1]_2 pho_chr3R_12589768_12589 0.00054 15_[-1]_119 pho_chr3R_12589777_12589 0.00054 6_[-1]_8 pho_chr3R_12725704_12725 0.00054 1_[-1]_2 pho_chr3R_12589801_12589 0.00054 6_[-1]_8 pho_chr3R_12589820_12589 0.00085 6_[-1]_8 pho_chr3R_12590048_12590 0.0016 6_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=12 pho_chr3R_12590084_12590 ( 9) ATGGCT 1 pho_chr3R_12590028_12590 ( 7) ATGGCT 1 pho_chr3R_12590026_12590 ( 7) ATGGCT 1 pho_chr3R_12589921_12589 ( 7) ATGGCT 1 pho_chr3R_12589924_12589 ( 4) ATGGCT 1 pho_chr3R_12725663_12725 ( 1) ATGGCT 1 pho_chr3R_12589768_12589 ( 16) ATGGCC 1 pho_chr3R_12589777_12589 ( 7) ATGGCC 1 pho_chr3R_12725704_12725 ( 2) ATGGCC 1 pho_chr3R_12589801_12589 ( 7) ATGGCC 1 pho_chr3R_12589820_12589 ( 7) ATGGCG 1 pho_chr3R_12590048_12590 ( 7) GTGGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 272 bayes= 4.43741 E= 1.5e-009 214 -1023 -180 -1023 -1023 -1023 -1023 226 -1023 -1023 178 -1023 -1023 -1023 178 -1023 -1023 178 -1023 -1023 -1023 51 -180 126 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 12 E= 1.5e-009 0.916667 0.000000 0.083333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.416667 0.083333 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- ATGGC[TC] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- pho_chr3R_12725663_12725 1.35e-03 8 pho_chr3R_12589924_12589 6.71e-03 20 pho_chr3R_12590048_12590 4.40e-02 19 pho_chr3R_12589801_12589 1.60e-02 20 pho_chr3R_12589921_12589 8.05e-03 23 pho_chr3R_12590026_12590 5.37e-03 17 pho_chr3R_12725704_12725 4.30e-03 9 pho_chr3R_12590028_12590 6.71e-03 20 pho_chr3R_12589820_12589 2.53e-02 20 pho_chr3R_12589777_12589 1.60e-02 20 pho_chr3R_12589768_12589 1.35e-01 140 pho_chr3R_12590084_12590 4.92e-03 16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************