******************************************************************************** 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/Deaf1_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Deaf1_chr2R_2013779_2013 1.0000 13 Deaf1_chr2R_2013635_2013 1.0000 53 Deaf1_chr2R_2013811_2013 1.0000 17 Deaf1_chr3R_2613192_2613 1.0000 51 Deaf1_chr2R_2013751_2013 1.0000 25 Deaf1_chr2R_2013718_2013 1.0000 10 Deaf1_chr2R_2013613_2013 1.0000 10 Deaf1_chr2R_2013899_2013 1.0000 12 Deaf1_chr3R_2613407_2613 1.0000 44 Deaf1_chr2R_2013856_2013 1.0000 12 ******************************************************************************** ******************************************************************************** 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/Deaf1_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= 10 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 247 N= 10 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.235 C 0.265 G 0.265 T 0.235 Background letter frequencies (from dataset with add-one prior applied): A 0.235 C 0.265 G 0.265 T 0.235 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 10 llr = 57 E-value = 7.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 25::a7 pos.-specific C 45a::: probability G 3::a:3 matrix T 1::::: bits 2.1 * 1.9 *** 1.7 *** 1.5 *** Information 1.3 **** content 1.0 ***** (8.2 bits) 0.8 ***** 0.6 ***** 0.4 ***** 0.2 ****** 0.0 ------ Multilevel CACGAA consensus GC G sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ Deaf1_chr2R_2013856_2013 - 3 2.42e-04 TCCC CACGAA AA Deaf1_chr3R_2613407_2613 - 28 2.42e-04 AAAATAATTA CACGAA TCACTTAAAT Deaf1_chr2R_2013751_2013 - 14 5.14e-04 GCCCCA CCCGAA GAGGTAGCCG Deaf1_chr3R_2613192_2613 + 42 5.14e-04 TCGCTTTTAG CCCGAA GCTT Deaf1_chr2R_2013718_2013 - 1 1.03e-03 GCCA GCCGAA Deaf1_chr2R_2013635_2013 + 2 1.24e-03 A AACGAA CGGCAGTTCG Deaf1_chr2R_2013613_2013 - 2 2.55e-03 TCC GACGAG C Deaf1_chr2R_2013811_2013 - 3 2.55e-03 CGACTGACT GACGAG TG Deaf1_chr2R_2013899_2013 - 3 3.10e-03 GAAT TCCGAA AC Deaf1_chr2R_2013779_2013 - 5 3.61e-03 TGG ACCGAG CGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Deaf1_chr2R_2013856_2013 0.00024 2_[-1]_4 Deaf1_chr3R_2613407_2613 0.00024 27_[-1]_11 Deaf1_chr2R_2013751_2013 0.00051 13_[-1]_6 Deaf1_chr3R_2613192_2613 0.00051 41_[+1]_4 Deaf1_chr2R_2013718_2013 0.001 [-1]_4 Deaf1_chr2R_2013635_2013 0.0012 1_[+1]_46 Deaf1_chr2R_2013613_2013 0.0025 1_[-1]_3 Deaf1_chr2R_2013811_2013 0.0025 2_[-1]_9 Deaf1_chr2R_2013899_2013 0.0031 2_[-1]_4 Deaf1_chr2R_2013779_2013 0.0036 4_[-1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=10 Deaf1_chr2R_2013856_2013 ( 3) CACGAA 1 Deaf1_chr3R_2613407_2613 ( 28) CACGAA 1 Deaf1_chr2R_2013751_2013 ( 14) CCCGAA 1 Deaf1_chr3R_2613192_2613 ( 42) CCCGAA 1 Deaf1_chr2R_2013718_2013 ( 1) GCCGAA 1 Deaf1_chr2R_2013635_2013 ( 2) AACGAA 1 Deaf1_chr2R_2013613_2013 ( 2) GACGAG 1 Deaf1_chr2R_2013811_2013 ( 3) GACGAG 1 Deaf1_chr2R_2013899_2013 ( 3) TCCGAA 1 Deaf1_chr2R_2013779_2013 ( 5) ACCGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 197 bayes= 5.20495 E= 7.3e-002 -23 59 18 -123 109 92 -997 -997 -997 192 -997 -997 -997 -997 192 -997 209 -997 -997 -997 157 -997 18 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 10 E= 7.3e-002 0.200000 0.400000 0.300000 0.100000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.700000 0.000000 0.300000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CGA][AC]CGA[AG] -------------------------------------------------------------------------------- Time 0.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Deaf1_chr2R_2013779_2013 5.62e-02 13 Deaf1_chr2R_2013635_2013 1.12e-01 53 Deaf1_chr2R_2013811_2013 5.94e-02 17 Deaf1_chr3R_2613192_2613 4.62e-02 51 Deaf1_chr2R_2013751_2013 2.03e-02 25 Deaf1_chr2R_2013718_2013 1.02e-02 10 Deaf1_chr2R_2013613_2013 2.52e-02 10 Deaf1_chr2R_2013899_2013 4.25e-02 12 Deaf1_chr3R_2613407_2613 1.87e-02 44 Deaf1_chr2R_2013856_2013 3.38e-03 12 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************