******************************************************************************** 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/Hsf_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Hsf_chr3L_3176658_317669 1.0000 42 Hsf_chr3R_7782498_778252 1.0000 26 Hsf_chr3R_7782302_778232 1.0000 27 Hsf_chr3R_7782428_778245 1.0000 25 Hsf_chr3R_7782329_778235 1.0000 27 ******************************************************************************** ******************************************************************************** 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/Hsf_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= 147 N= 5 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.241 G 0.241 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.242 G 0.242 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 15 sites = 5 llr = 70 E-value = 1.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:4:8822::::6:a pos.-specific C 6:6::::2::a:4:: probability G :4:a::42:::4:a: matrix T :6::2244aa:6::: bits 2.0 * *** ** 1.8 * *** ** 1.6 * *** ** 1.4 * *** ** Information 1.2 *** *** ** content 1.0 ****** ******* (20.1 bits) 0.8 ****** ******* 0.6 ****** ******* 0.4 ******* ******* 0.2 ******* ******* 0.0 --------------- Multilevel CTCGAAGTTTCTAGA consensus AGA TTTA GC sequence AC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- Hsf_chr3L_3176658_317669 + 20 1.02e-08 CCAGAAGCCT CTAGAAGTTTCTAGA GACTTCCA Hsf_chr3R_7782302_778232 + 4 1.09e-07 CGC CTCGAATGTTCGCGA AAAGAGCGC Hsf_chr3R_7782498_778252 + 7 1.76e-07 AAATAA AGCGAATATTCTAGA ATCCC Hsf_chr3R_7782428_778245 - 5 4.21e-07 ACGGCC AGAGAAATTTCTCGA GTTT Hsf_chr3R_7782329_778235 + 8 1.09e-06 CACTGTT CTCGTTGCTTCGAGA GAGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Hsf_chr3L_3176658_317669 1e-08 19_[+1]_8 Hsf_chr3R_7782302_778232 1.1e-07 3_[+1]_9 Hsf_chr3R_7782498_778252 1.8e-07 6_[+1]_5 Hsf_chr3R_7782428_778245 4.2e-07 4_[-1]_6 Hsf_chr3R_7782329_778235 1.1e-06 7_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=5 Hsf_chr3L_3176658_317669 ( 20) CTAGAAGTTTCTAGA 1 Hsf_chr3R_7782302_778232 ( 4) CTCGAATGTTCGCGA 1 Hsf_chr3R_7782498_778252 ( 7) AGCGAATATTCTAGA 1 Hsf_chr3R_7782428_778245 ( 5) AGAGAAATTTCTCGA 1 Hsf_chr3R_7782329_778235 ( 8) CTCGTTGCTTCGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 77 bayes= 3.848 E= 1.2e-002 63 131 -897 -897 -897 -897 73 121 63 131 -897 -897 -897 -897 205 -897 163 -897 -897 -37 163 -897 -897 -37 -37 -897 73 63 -37 -27 -27 63 -897 -897 -897 195 -897 -897 -897 195 -897 205 -897 -897 -897 -897 73 121 121 73 -897 -897 -897 -897 205 -897 195 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 1.2e-002 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.400000 0.400000 0.200000 0.200000 0.200000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.600000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][TG][CA]G[AT][AT][GTA][TACGA]TTC[TG][AC]GA -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- Hsf_chr3L_3176658_317669 5.72e-07 19_[+1(1.02e-08)]_8 Hsf_chr3R_7782498_778252 4.21e-06 6_[+1(1.76e-07)]_5 Hsf_chr3R_7782302_778232 2.84e-06 3_[+1(1.09e-07)]_9 Hsf_chr3R_7782428_778245 9.26e-06 4_[-1(4.21e-07)]_6 Hsf_chr3R_7782329_778235 2.84e-05 7_[+1(1.09e-06)]_5 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************