******************************************************************************** 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/p120_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ p120_chr3L_8700293_87003 1.0000 33 p120_chr3L_8700136_87001 1.0000 28 p120_chr3L_8700197_87002 1.0000 17 ******************************************************************************** ******************************************************************************** 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/p120_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= 3 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 78 N= 3 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.365 C 0.135 G 0.135 T 0.365 Background letter frequencies (from dataset with add-one prior applied): A 0.360 C 0.140 G 0.140 T 0.360 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 2 llr = 18 E-value = 5.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::5::a pos.-specific C :a:5a: probability G a:55:: matrix T :::::: bits 2.8 ** * 2.6 ** * 2.3 ** * 2.0 ** * Information 1.7 ** ** content 1.4 ** *** (13.0 bits) 1.1 ****** 0.9 ****** 0.6 ****** 0.3 ****** 0.0 ------ Multilevel GCACCA consensus GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ p120_chr3L_8700197_87002 + 1 3.90e-05 . GCGCCA ATTGAATGTT p120_chr3L_8700293_87003 + 26 1.39e-04 TTCTACCAAC GCAGCA GA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- p120_chr3L_8700197_87002 3.9e-05 [+1]_11 p120_chr3L_8700293_87003 0.00014 25_[+1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=2 p120_chr3L_8700197_87002 ( 1) GCGCCA 1 p120_chr3L_8700293_87003 ( 26) GCAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 63 bayes= 4.93074 E= 5.6e+001 -765 -765 283 -765 -765 283 -765 -765 47 -765 183 -765 -765 183 183 -765 -765 283 -765 -765 147 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 2 E= 5.6e+001 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GC[AG][CG]CA -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- p120_chr3L_8700293_87003 7.76e-03 33 p120_chr3L_8700136_87001 9.99e-01 28 p120_chr3L_8700197_87002 9.37e-04 [+1(3.90e-05)]_11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************