******************************************************************************** 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/gl_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ gl_chr3R_15714115_157141 1.0000 24 gl_chr3R_14200860_142009 1.0000 54 gl_chr3R_15714233_157142 1.0000 51 gl_chr3R_15714205_157142 1.0000 16 gl_chr3R_14200938_142009 1.0000 16 ******************************************************************************** ******************************************************************************** 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/gl_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= 5 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 161 N= 5 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from dataset with add-one prior applied): A 0.303 C 0.197 G 0.197 T 0.303 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 11 sites = 5 llr = 44 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a:::286:26: pos.-specific C ::::42::2:: probability G :2:24::844: matrix T :8a8::422:a bits 2.3 2.1 1.9 1.6 * * * Information 1.4 * * * * content 1.2 **** * * * (12.7 bits) 0.9 **** * * ** 0.7 ******** ** 0.5 ******** ** 0.2 *********** 0.0 ----------- Multilevel ATTTCAAGGAT consensus G GGCTTAG sequence A C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------- gl_chr3R_15714115_157141 + 9 1.79e-06 TTAAAGGC ATTTCAAGGGT TTCCA gl_chr3R_15714233_157142 + 1 1.76e-05 . ATTTGAAGAAT ATTATGAAAA gl_chr3R_14200860_142009 - 14 6.55e-05 CCCGAAAAGT ATTTCATTGAT TTTAGAAGCC gl_chr3R_15714205_157142 + 4 9.67e-05 GCG ATTTAATGTGT CA gl_chr3R_14200938_142009 - 2 1.63e-04 CTTG AGTGGCAGCAT A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- gl_chr3R_15714115_157141 1.8e-06 8_[+1]_5 gl_chr3R_15714233_157142 1.8e-05 [+1]_40 gl_chr3R_14200860_142009 6.5e-05 13_[-1]_30 gl_chr3R_15714205_157142 9.7e-05 3_[+1]_2 gl_chr3R_14200938_142009 0.00016 1_[-1]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=11 seqs=5 gl_chr3R_15714115_157141 ( 9) ATTTCAAGGGT 1 gl_chr3R_15714233_157142 ( 1) ATTTGAAGAAT 1 gl_chr3R_14200860_142009 ( 14) ATTTCATTGAT 1 gl_chr3R_15714205_157142 ( 4) ATTTAATGTGT 1 gl_chr3R_14200938_142009 ( 2) AGTGGCAGCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 111 bayes= 4.66838 E= 1.1e+002 172 -897 -897 -897 -897 -897 2 140 -897 -897 -897 172 -897 -897 2 140 -60 102 102 -897 140 2 -897 -897 98 -897 -897 40 -897 -897 202 -60 -60 2 102 -60 98 -897 102 -897 -897 -897 -897 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5 E= 1.1e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.400000 0.400000 0.000000 0.800000 0.200000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.000000 0.800000 0.200000 0.200000 0.200000 0.400000 0.200000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[TG]T[TG][CGA][AC][AT][GT][GACTA][AG]T -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- gl_chr3R_15714115_157141 5.02e-05 8_[+1(1.79e-06)]_5 gl_chr3R_14200860_142009 5.74e-03 13_[-1(6.55e-05)]_30 gl_chr3R_15714233_157142 1.44e-03 [+1(1.76e-05)]_40 gl_chr3R_15714205_157142 1.16e-03 3_[+1(9.67e-05)]_2 gl_chr3R_14200938_142009 1.96e-03 16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************