******************************************************************************** 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/bab1_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ bab1_chr3L_1069304_10693 1.0000 15 bab1_chr3L_1069333_10693 1.0000 20 bab1_chr3L_1069513_10695 1.0000 20 bab1_chr3L_1159056_11590 1.0000 26 bab1_chr3L_1069625_10696 1.0000 25 bab1_chr3L_1159108_11591 1.0000 15 ******************************************************************************** ******************************************************************************** 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/bab1_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= 6 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 121 N= 6 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.426 C 0.074 G 0.074 T 0.426 Background letter frequencies (from dataset with add-one prior applied): A 0.420 C 0.080 G 0.080 T 0.420 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 6 llr = 47 E-value = 2.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2332a:373:7:: pos.-specific C 5:::::::::::: probability G 32:::::2::3:3 matrix T :578:a727a:a7 bits 3.6 3.3 2.9 2.6 Information 2.2 content 1.8 * (11.2 bits) 1.5 * 1.1 * ** **** 0.7 * *** **** 0.4 ************* 0.0 ------------- Multilevel CTTTATTATTATT consensus GAA A A G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- bab1_chr3L_1069333_10693 - 3 2.75e-06 CACAT CTATATAGTTGTG CA bab1_chr3L_1069625_10696 + 11 4.25e-06 TCGTTAATAG CGTTATTAATGTT AT bab1_chr3L_1159108_11591 + 3 4.40e-05 AT GTTTATTATTATT bab1_chr3L_1069513_10695 - 4 3.25e-04 AAAA GATAATTATTATT TAT bab1_chr3L_1159056_11590 + 9 3.95e-04 TTAATTAT ATTTATTATTATT GTTAT bab1_chr3L_1069304_10693 + 3 3.95e-04 TA CAATATATATATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bab1_chr3L_1069333_10693 2.8e-06 2_[-1]_5 bab1_chr3L_1069625_10696 4.2e-06 10_[+1]_2 bab1_chr3L_1159108_11591 4.4e-05 2_[+1] bab1_chr3L_1069513_10695 0.00032 3_[-1]_4 bab1_chr3L_1159056_11590 0.0004 8_[+1]_5 bab1_chr3L_1069304_10693 0.0004 2_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=6 bab1_chr3L_1069333_10693 ( 3) CTATATAGTTGTG 1 bab1_chr3L_1069625_10696 ( 11) CGTTATTAATGTT 1 bab1_chr3L_1159108_11591 ( 3) GTTTATTATTATT 1 bab1_chr3L_1069513_10695 ( 4) GATAATTATTATT 1 bab1_chr3L_1159056_11590 ( 9) ATTTATTATTATT 1 bab1_chr3L_1069304_10693 ( 3) CAATATATATATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 49 bayes= 3.34147 E= 2.9e+001 -133 264 206 -923 -33 -923 106 25 -33 -923 -923 67 -133 -923 -923 99 125 -923 -923 -923 -923 -923 -923 125 -33 -923 -923 67 67 -923 106 -133 -33 -923 -923 67 -923 -923 -923 125 67 -923 206 -923 -923 -923 -923 125 -923 -923 206 67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 6 E= 2.9e+001 0.166667 0.500000 0.333333 0.000000 0.333333 0.000000 0.166667 0.500000 0.333333 0.000000 0.000000 0.666667 0.166667 0.000000 0.000000 0.833333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.666667 0.000000 0.166667 0.166667 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][TA][TA]TAT[TA]A[TA]T[AG]T[TG] -------------------------------------------------------------------------------- Time 0.05 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bab1_chr3L_1069304_10693 2.37e-03 15 bab1_chr3L_1069333_10693 4.40e-05 2_[-1(2.75e-06)]_5 bab1_chr3L_1069513_10695 5.18e-03 20 bab1_chr3L_1159056_11590 1.10e-02 26 bab1_chr3L_1069625_10696 1.10e-04 10_[+1(4.25e-06)]_2 bab1_chr3L_1159108_11591 2.64e-04 2_[+1(4.40e-05)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************