******************************************************************************** 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/byn_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ byn_chr2R_16406726_16406 1.0000 24 byn_chr2R_16406990_16407 1.0000 17 byn_chr2R_16407702_16407 1.0000 23 byn_chr2R_16406573_16406 1.0000 19 byn_chr2R_16406967_16406 1.0000 15 byn_chr2R_16406874_16406 1.0000 31 byn_chr2R_16407819_16407 1.0000 19 byn_chr2R_16407647_16407 1.0000 29 byn_chr2R_16406263_16406 1.0000 24 ******************************************************************************** ******************************************************************************** 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/byn_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= 9 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 201 N= 9 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.299 C 0.201 G 0.201 T 0.299 Background letter frequencies (from dataset with add-one prior applied): A 0.298 C 0.202 G 0.202 T 0.298 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 9 llr = 75 E-value = 2.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 841::128462:: pos.-specific C 2::1:8:12::42 probability G :37:a:41:::11 matrix T :229:13:34847 bits 2.3 * 2.1 * 1.8 * 1.6 * Information 1.4 ** content 1.2 * *** (12.0 bits) 0.9 * **** * * 0.7 * **** * **** 0.5 ******** **** 0.2 ************* 0.0 ------------- Multilevel AAGTGCGAAATCT consensus CGT T TTATC sequence T A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- byn_chr2R_16406573_16406 + 4 1.15e-07 GTT AGGTGCGATATCT CCA byn_chr2R_16406726_16406 + 4 6.67e-07 AAG AAGTGCGACTTTT AACATCCA byn_chr2R_16406263_16406 + 4 1.48e-06 GGA AAGTGCTAATTTT TACACATA byn_chr2R_16406874_16406 - 17 5.73e-06 CT AAGTGCGATTTCG AGAAGTGGCG byn_chr2R_16407647_16407 + 17 1.84e-04 CGCGCAAGCA ATTTGCACAATTT byn_chr2R_16407702_16407 + 8 2.10e-04 GAGCGAA CGACGCGATTTCT CCC byn_chr2R_16406990_16407 - 1 2.24e-04 ATTT ATGTGTTACAACT byn_chr2R_16406967_16406 - 1 2.86e-04 CG AGGTGAAAAAATC byn_chr2R_16407819_16407 - 5 5.37e-04 CA CATTGCTGAATGC ACAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- byn_chr2R_16406573_16406 1.2e-07 3_[+1]_3 byn_chr2R_16406726_16406 6.7e-07 3_[+1]_8 byn_chr2R_16406263_16406 1.5e-06 3_[+1]_8 byn_chr2R_16406874_16406 5.7e-06 16_[-1]_2 byn_chr2R_16407647_16407 0.00018 16_[+1] byn_chr2R_16407702_16407 0.00021 7_[+1]_3 byn_chr2R_16406990_16407 0.00022 [-1]_4 byn_chr2R_16406967_16406 0.00029 [-1]_2 byn_chr2R_16407819_16407 0.00054 4_[-1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=9 byn_chr2R_16406573_16406 ( 4) AGGTGCGATATCT 1 byn_chr2R_16406726_16406 ( 4) AAGTGCGACTTTT 1 byn_chr2R_16406263_16406 ( 4) AAGTGCTAATTTT 1 byn_chr2R_16406874_16406 ( 17) AAGTGCGATTTCG 1 byn_chr2R_16407647_16407 ( 17) ATTTGCACAATTT 1 byn_chr2R_16407702_16407 ( 8) CGACGCGATTTCT 1 byn_chr2R_16406990_16407 ( 1) ATGTGTTACAACT 1 byn_chr2R_16406967_16406 ( 1) AGGTGAAAAAATC 1 byn_chr2R_16407819_16407 ( 5) CATTGCTGAATGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 93 bayes= 3.37037 E= 2.9e-002 139 13 -982 -982 58 -982 72 -42 -142 -982 172 -42 -982 -86 -982 158 -982 -982 230 -982 -142 194 -982 -142 -42 -982 113 16 139 -86 -86 -982 58 13 -982 16 90 -982 -982 58 -42 -982 -982 139 -982 113 -86 58 -982 13 -86 116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 9 E= 2.9e-002 0.777778 0.222222 0.000000 0.000000 0.444444 0.000000 0.333333 0.222222 0.111111 0.000000 0.666667 0.222222 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 1.000000 0.000000 0.111111 0.777778 0.000000 0.111111 0.222222 0.000000 0.444444 0.333333 0.777778 0.111111 0.111111 0.000000 0.444444 0.222222 0.000000 0.333333 0.555556 0.000000 0.000000 0.444444 0.222222 0.000000 0.000000 0.777778 0.000000 0.444444 0.111111 0.444444 0.000000 0.222222 0.111111 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AGT][GT]TGC[GTA]A[ATC][AT][TA][CT][TC] -------------------------------------------------------------------------------- Time 0.08 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- byn_chr2R_16406726_16406 1.60e-05 3_[+1(6.67e-07)]_8 byn_chr2R_16406990_16407 2.24e-03 17 byn_chr2R_16407702_16407 4.60e-03 23 byn_chr2R_16406573_16406 1.61e-06 3_[+1(1.15e-07)]_3 byn_chr2R_16406967_16406 1.72e-03 15 byn_chr2R_16406874_16406 2.18e-04 16_[-1(5.73e-06)]_2 byn_chr2R_16407819_16407 7.50e-03 19 byn_chr2R_16407647_16407 6.23e-03 29 byn_chr2R_16406263_16406 3.56e-05 3_[+1(1.48e-06)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************