******************************************************************************** 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/brk_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ brk_chr3R_2581266_258127 1.0000 12 brk_chr3R_2580051_258006 1.0000 16 brk_chrX_4231706_4231722 1.0000 17 brk_chr3R_2580282_258029 1.0000 13 brk_chr3R_2507579_250759 1.0000 18 brk_chr3R_20575223_20575 1.0000 7 brk_chr2L_11454460_11454 1.0000 18 brk_chr2L_11454379_11454 1.0000 18 brk_chr3R_20574945_20574 1.0000 7 brk_chr3R_2580553_258056 1.0000 16 brk_chr3R_2507229_250724 1.0000 16 brk_chr3R_2580147_258016 1.0000 14 brk_chr3R_2580196_258020 1.0000 13 brk_chr3R_20574932_20574 1.0000 7 brk_chr3R_2507343_250737 1.0000 34 ******************************************************************************** ******************************************************************************** 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/brk_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= 15 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 226 N= 15 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.168 C 0.332 G 0.332 T 0.168 Background letter frequencies (from dataset with add-one prior applied): A 0.170 C 0.330 G 0.330 T 0.170 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 15 llr = 88 E-value = 1.5e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::11 pos.-specific C 1::a:5 probability G :aa:91 matrix T 9::::2 bits 2.6 2.3 2.0 * 1.8 * Information 1.5 **** content 1.3 ***** (8.4 bits) 1.0 ***** 0.8 ***** 0.5 ***** 0.3 ****** 0.0 ------ Multilevel TGGCGC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ brk_chr3R_2507229_250724 - 9 6.68e-04 CA TGGCGC TAAACAGA brk_chr3R_2580553_258056 + 7 6.68e-04 TATTAC TGGCGC TATC brk_chr3R_20574945_20574 + 1 6.68e-04 . TGGCGC T brk_chr2L_11454379_11454 + 6 6.68e-04 ATGAA TGGCGC CCACCGC brk_chr2L_11454460_11454 + 7 6.68e-04 TCCAAG TGGCGC TTAGGC brk_chrX_4231706_4231722 + 7 6.68e-04 GCTTGG TGGCGC CTCAA brk_chr3R_2507343_250737 - 9 1.01e-03 CCCATCAACT TGGCGT CAGCTTGT brk_chr3R_20574932_20574 + 1 1.01e-03 . TGGCGT G brk_chr3R_2580147_258016 + 3 1.01e-03 TC TGGCGT TGCGTG brk_chr3R_2580196_258020 - 7 1.35e-03 C TGGCGA GACTCC brk_chr3R_20575223_20575 + 1 1.35e-03 . TGGCGA T brk_chr3R_2580282_258029 + 4 2.02e-03 CGG TGGCGG CGCT brk_chr3R_2581266_258127 + 3 2.02e-03 CC TGGCGG CGCC brk_chr3R_2580051_258006 + 7 2.36e-03 CCCGAC TGGCAC CTCG brk_chr3R_2507579_250759 + 8 4.36e-03 GATTGCC CGGCGC CGACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- brk_chr3R_2507229_250724 0.00067 8_[-1]_2 brk_chr3R_2580553_258056 0.00067 6_[+1]_4 brk_chr3R_20574945_20574 0.00067 [+1]_1 brk_chr2L_11454379_11454 0.00067 5_[+1]_7 brk_chr2L_11454460_11454 0.00067 6_[+1]_6 brk_chrX_4231706_4231722 0.00067 6_[+1]_5 brk_chr3R_2507343_250737 0.001 8_[-1]_20 brk_chr3R_20574932_20574 0.001 [+1]_1 brk_chr3R_2580147_258016 0.001 2_[+1]_6 brk_chr3R_2580196_258020 0.0014 6_[-1]_1 brk_chr3R_20575223_20575 0.0014 [+1]_1 brk_chr3R_2580282_258029 0.002 3_[+1]_4 brk_chr3R_2581266_258127 0.002 2_[+1]_4 brk_chr3R_2580051_258006 0.0024 6_[+1]_4 brk_chr3R_2507579_250759 0.0044 7_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=15 brk_chr3R_2507229_250724 ( 9) TGGCGC 1 brk_chr3R_2580553_258056 ( 7) TGGCGC 1 brk_chr3R_20574945_20574 ( 1) TGGCGC 1 brk_chr2L_11454379_11454 ( 6) TGGCGC 1 brk_chr2L_11454460_11454 ( 7) TGGCGC 1 brk_chrX_4231706_4231722 ( 7) TGGCGC 1 brk_chr3R_2507343_250737 ( 9) TGGCGT 1 brk_chr3R_20574932_20574 ( 1) TGGCGT 1 brk_chr3R_2580147_258016 ( 3) TGGCGT 1 brk_chr3R_2580196_258020 ( 7) TGGCGA 1 brk_chr3R_20575223_20575 ( 1) TGGCGA 1 brk_chr3R_2580282_258029 ( 4) TGGCGG 1 brk_chr3R_2581266_258127 ( 3) TGGCGG 1 brk_chr3R_2580051_258006 ( 7) TGGCAC 1 brk_chr3R_2507579_250759 ( 8) CGGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 151 bayes= 4.54565 E= 1.5e-010 -1055 -231 -1055 246 -1055 -1055 160 -1055 -1055 -1055 160 -1055 -1055 160 -1055 -1055 -135 -1055 150 -1055 -35 69 -131 24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 15 E= 1.5e-010 0.000000 0.066667 0.000000 0.933333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.066667 0.000000 0.933333 0.000000 0.133333 0.533333 0.133333 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TGGCG[CT] -------------------------------------------------------------------------------- Time 0.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- brk_chr3R_2581266_258127 2.79e-02 12 brk_chr3R_2580051_258006 5.07e-02 16 brk_chrX_4231706_4231722 1.59e-02 17 brk_chr3R_2580282_258029 3.19e-02 13 brk_chr3R_2507579_250759 1.07e-01 18 brk_chr3R_20575223_20575 5.40e-03 7 brk_chr2L_11454460_11454 1.72e-02 18 brk_chr2L_11454379_11454 1.72e-02 18 brk_chr3R_20574945_20574 2.67e-03 7 brk_chr3R_2580553_258056 1.46e-02 16 brk_chr3R_2507229_250724 1.46e-02 16 brk_chr3R_2580147_258016 1.80e-02 14 brk_chr3R_2580196_258020 2.14e-02 13 brk_chr3R_20574932_20574 4.04e-03 7 brk_chr3R_2507343_250737 5.70e-02 34 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************