******************************************************************************** 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/prd_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ prd_chr2R_20564846_20564 1.0000 16 prd_chr2R_20564632_20564 1.0000 19 prd_chr2R_20564499_20564 1.0000 19 prd_chr2R_20564213_20564 1.0000 19 prd_chr2R_20564927_20564 1.0000 25 prd_chr2R_5490991_549101 1.0000 27 prd_chr2R_5490918_549095 1.0000 33 prd_chr2R_20564267_20564 1.0000 18 prd_chr2R_20564538_20564 1.0000 13 prd_chr2R_20564736_20564 1.0000 36 prd_chr2R_20564465_20564 1.0000 28 ******************************************************************************** ******************************************************************************** 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/prd_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= 253 N= 11 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.231 G 0.231 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.232 G 0.232 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 9 llr = 61 E-value = 3.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6::3:a8 pos.-specific C 7:9628:2 probability G :41442:: matrix T 3::::::: bits 2.1 1.9 * 1.7 * * 1.5 * * Information 1.3 * *** content 1.1 **** *** (9.8 bits) 0.8 **** *** 0.6 **** *** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CACCGCAA consensus TG GAG C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- prd_chr2R_20564538_20564 - 5 1.29e-05 A CACCGCAA TTAT prd_chr2R_20564499_20564 + 12 1.42e-04 ATAACTAAAT TACCGCAA prd_chr2R_20564927_20564 + 16 1.68e-04 ATCGATTTGA CACGCCAA CG prd_chr2R_5490991_549101 + 1 2.18e-04 . CACCGCAC GATTAGCACC prd_chr2R_20564465_20564 - 5 2.84e-04 ATGCGATTTT CGCCGGAA ATTG prd_chr2R_20564736_20564 - 9 4.02e-04 CCCCTAATCA TGCGACAA AAAGTGGA prd_chr2R_20564632_20564 + 12 5.41e-04 AAACCATTAA CACCCGAA prd_chr2R_20564846_20564 + 7 1.00e-03 GGTCGC TGCGACAC GG prd_chr2R_5490918_549095 - 15 1.07e-03 GATAACGAGG CGGGACAA AGCGGAGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- prd_chr2R_20564538_20564 1.3e-05 4_[-1]_1 prd_chr2R_20564499_20564 0.00014 11_[+1] prd_chr2R_20564927_20564 0.00017 15_[+1]_2 prd_chr2R_5490991_549101 0.00022 [+1]_19 prd_chr2R_20564465_20564 0.00028 4_[-1]_16 prd_chr2R_20564736_20564 0.0004 8_[-1]_20 prd_chr2R_20564632_20564 0.00054 11_[+1] prd_chr2R_20564846_20564 0.001 6_[+1]_2 prd_chr2R_5490918_549095 0.0011 14_[-1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=9 prd_chr2R_20564538_20564 ( 5) CACCGCAA 1 prd_chr2R_20564499_20564 ( 12) TACCGCAA 1 prd_chr2R_20564927_20564 ( 16) CACGCCAA 1 prd_chr2R_5490991_549101 ( 1) CACCGCAC 1 prd_chr2R_20564465_20564 ( 5) CGCCGGAA 1 prd_chr2R_20564736_20564 ( 9) TGCGACAA 1 prd_chr2R_20564632_20564 ( 12) CACCCGAA 1 prd_chr2R_20564846_20564 ( 7) TGCGACAC 1 prd_chr2R_5490918_549095 ( 15) CGGGACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 176 bayes= 4.35497 E= 3.0e+001 -982 152 -982 31 105 -982 94 -982 -982 194 -106 -982 -982 126 94 -982 31 -6 94 -982 -982 175 -6 -982 190 -982 -982 -982 153 -6 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 3.0e+001 0.000000 0.666667 0.000000 0.333333 0.555556 0.000000 0.444444 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.555556 0.444444 0.000000 0.333333 0.222222 0.444444 0.000000 0.000000 0.777778 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.222222 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][AG]C[CG][GAC][CG]A[AC] -------------------------------------------------------------------------------- Time 0.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- prd_chr2R_20564846_20564 1.79e-02 16 prd_chr2R_20564632_20564 1.29e-02 19 prd_chr2R_20564499_20564 3.41e-03 19 prd_chr2R_20564213_20564 1.00e+00 19 prd_chr2R_20564927_20564 6.04e-03 25 prd_chr2R_5490991_549101 8.69e-03 27 prd_chr2R_5490918_549095 5.40e-02 33 prd_chr2R_20564267_20564 8.06e-01 18 prd_chr2R_20564538_20564 1.54e-04 4_[-1(1.29e-05)]_1 prd_chr2R_20564736_20564 2.30e-02 36 prd_chr2R_20564465_20564 1.19e-02 28 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************