******************************************************************************** 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/Abd-B_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Abd-B_chr3R_9724615_9724 1.0000 10 Abd-B_chr3R_9724527_9724 1.0000 10 Abd-B_chr3R_9724092_9724 1.0000 11 Abd-B_chr3R_9723999_9724 1.0000 10 Abd-B_chr3R_9723844_9723 1.0000 10 Abd-B_chr3R_9724558_9724 1.0000 10 Abd-B_chr3R_9723807_9723 1.0000 10 ******************************************************************************** ******************************************************************************** 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/Abd-B_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= 11 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 7 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 71 N= 7 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.380 C 0.120 G 0.120 T 0.380 Background letter frequencies (from dataset with add-one prior applied): A 0.373 C 0.127 G 0.127 T 0.373 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 7 llr = 44 E-value = 2.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4119:aa9 pos.-specific C 137::::: probability G 4:11:::: matrix T :6::a::1 bits 3.0 2.7 2.4 2.1 Information 1.8 content 1.5 * *** (9.1 bits) 1.2 ***** 0.9 * ****** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel ATCATAAA consensus GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- Abd-B_chr3R_9724092_9724 + 2 5.82e-05 T GTCATAAA AA Abd-B_chr3R_9724615_9724 - 2 6.32e-05 A GCCGTAAA A Abd-B_chr3R_9723807_9723 + 2 3.08e-04 G CTCATAAA T Abd-B_chr3R_9724558_9724 - 2 3.08e-04 G ATCATAAA A Abd-B_chr3R_9724527_9724 - 2 3.08e-04 A ATCATAAA A Abd-B_chr3R_9723844_9723 + 2 3.00e-03 A ACGATAAT G Abd-B_chr3R_9723999_9724 - 2 3.00e-03 C GAAATAAA A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Abd-B_chr3R_9724092_9724 5.8e-05 1_[+1]_2 Abd-B_chr3R_9724615_9724 6.3e-05 1_[-1]_1 Abd-B_chr3R_9723807_9723 0.00031 1_[+1]_1 Abd-B_chr3R_9724558_9724 0.00031 1_[-1]_1 Abd-B_chr3R_9724527_9724 0.00031 1_[-1]_1 Abd-B_chr3R_9723844_9723 0.003 1_[+1]_1 Abd-B_chr3R_9723999_9724 0.003 1_[-1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=7 Abd-B_chr3R_9724092_9724 ( 2) GTCATAAA 1 Abd-B_chr3R_9724615_9724 ( 2) GCCGTAAA 1 Abd-B_chr3R_9723807_9723 ( 2) CTCATAAA 1 Abd-B_chr3R_9724558_9724 ( 2) ATCATAAA 1 Abd-B_chr3R_9724527_9724 ( 2) ATCATAAA 1 Abd-B_chr3R_9723844_9723 ( 2) ACGATAAT 1 Abd-B_chr3R_9723999_9724 ( 2) GAAATAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 22 bayes= 2.66297 E= 2.3e-003 20 17 176 -945 -138 117 -945 61 -138 249 17 -945 120 -945 17 -945 -945 -945 -945 142 142 -945 -945 -945 142 -945 -945 -945 120 -945 -945 -138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.3e-003 0.428571 0.142857 0.428571 0.000000 0.142857 0.285714 0.000000 0.571429 0.142857 0.714286 0.142857 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG][TC]CATAAA -------------------------------------------------------------------------------- Time 0.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Abd-B_chr3R_9724615_9724 3.79e-04 1_[-1(6.32e-05)]_1 Abd-B_chr3R_9724527_9724 1.84e-03 10 Abd-B_chr3R_9724092_9724 4.65e-04 1_[+1(5.82e-05)]_2 Abd-B_chr3R_9723999_9724 1.79e-02 10 Abd-B_chr3R_9723844_9723 1.79e-02 10 Abd-B_chr3R_9724558_9724 1.84e-03 10 Abd-B_chr3R_9723807_9723 1.84e-03 10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************