******************************************************************************** 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/Antp_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Antp_chr2R_1216998_12170 1.0000 37 Antp_chr2L_21840808_2184 1.0000 21 Antp_chr2R_1217540_12175 1.0000 33 Antp_chr2R_1217467_12174 1.0000 15 Antp_chr2L_21840884_2184 1.0000 20 Antp_chr2R_1217374_12173 1.0000 17 Antp_chr2L_21840626_2184 1.0000 16 Antp_chr3R_2831032_28310 1.0000 41 Antp_chr2L_21840736_2184 1.0000 13 Antp_chr3R_2830986_28310 1.0000 42 Antp_chr2R_1217428_12174 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/Antp_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= 11 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 265 N= 11 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.413 C 0.087 G 0.087 T 0.413 Background letter frequencies (from dataset with add-one prior applied): A 0.411 C 0.089 G 0.089 T 0.411 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 2 llr = 20 E-value = 7.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::55 pos.-specific C :::a:5 probability G :aa:5: matrix T a::::: bits 3.5 *** 3.1 *** 2.8 *** 2.4 *** Information 2.1 *** content 1.7 *** (14.5 bits) 1.4 ****** 1.0 ****** 0.7 ****** 0.3 ****** 0.0 ------ Multilevel TGGCAA consensus GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ Antp_chr2R_1216998_12170 + 26 2.32e-06 TCAAAATAAT TGGCGC ATTTCA Antp_chr2R_1217540_12175 - 18 7.29e-05 CTCTTTTACA TGGCAA TAATCATAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Antp_chr2R_1216998_12170 2.3e-06 25_[+1]_6 Antp_chr2R_1217540_12175 7.3e-05 17_[-1]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=2 Antp_chr2R_1216998_12170 ( 26) TGGCGC 1 Antp_chr2R_1217540_12175 ( 18) TGGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 210 bayes= 6.70044 E= 7.9e+002 -765 -765 -765 128 -765 -765 348 -765 -765 -765 348 -765 -765 348 -765 -765 28 -765 248 -765 28 248 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 2 E= 7.9e+002 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 0.500000 0.000000 0.500000 0.000000 0.500000 0.500000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TGGC[AG][AC] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- Antp_chr2R_1216998_12170 1.49e-04 25_[+1(2.32e-06)]_6 Antp_chr2L_21840808_2184 8.14e-01 21 Antp_chr2R_1217540_12175 4.08e-03 17_[-1(7.29e-05)]_10 Antp_chr2R_1217467_12174 4.92e-01 15 Antp_chr2L_21840884_2184 9.91e-01 20 Antp_chr2R_1217374_12173 9.95e-01 17 Antp_chr2L_21840626_2184 5.25e-01 16 Antp_chr3R_2831032_28310 1.00e+00 41 Antp_chr2L_21840736_2184 2.51e-01 13 Antp_chr3R_2830986_28310 1.00e+00 42 Antp_chr2R_1217428_12174 7.93e-01 10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************