******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2004/08/18 09:07:01) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. 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.sdsc.edu. ******************************************************************************** ******************************************************************************** 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= INO_up800.s ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ CHO1 1.0000 800 CHO2 1.0000 800 FAS1 1.0000 800 FAS2 1.0000 800 ACC1 1.0000 800 INO1 1.0000 800 OPI3 1.0000 800 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.nc.6.freq INO_up800.s model: mod= oops nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 7 maxsites= 7 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 5600 N= 7 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 yeast.nc.6.freq): A 0.324 C 0.176 G 0.176 T 0.324 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 12 sites = 7 llr = 95 E-value = 2.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::9:a::::3: pos.-specific C ::a:9:11691a probability G ::::1::94:4: matrix T aa:1::9::11: bits 2.5 * * 2.3 * * 2.0 * * * * 1.8 * * * * * Information 1.5 *** ** *** * content 1.3 *** ****** * (19.5 bits) 1.0 ********** * 0.8 ********** * 0.5 ********** * 0.3 ************ 0.0 ------------ Multilevel TTCACATGCCGC consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ INO1 - 620 1.85e-08 GACAATACTT TTCACATGCCGC ATTTAGCCGC FAS1 + 95 1.85e-08 GGCCAAAAAC TTCACATGCCGC CCAGCCAAGC ACC1 + 83 1.52e-07 CGTTAAAATC TTCACATGGCCC GGCCGCGCGC CHO2 + 354 2.52e-07 TGCCACACTT TTCTCATGCCGC ATTCATTATT CHO1 + 611 4.23e-07 ACTTTGAACG TTCACACGGCAC CCTCACGCCT FAS2 + 567 9.43e-07 CTCCCGCGTT TTCACATGCTAC CTCATTCGCC OPI3 + 340 3.32e-06 CCAAGCCTCC TTCAGATCGCTC TTGTCGACCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- INO1 1.8e-08 619_[-1]_169 FAS1 1.8e-08 94_[+1]_694 ACC1 1.5e-07 82_[+1]_706 CHO2 2.5e-07 353_[+1]_435 CHO1 4.2e-07 610_[+1]_178 FAS2 9.4e-07 566_[+1]_222 OPI3 3.3e-06 339_[+1]_449 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=7 INO1 ( 620) TTCACATGCCGC 1 FAS1 ( 95) TTCACATGCCGC 1 ACC1 ( 83) TTCACATGGCCC 1 CHO2 ( 354) TTCTCATGCCGC 1 CHO1 ( 611) TTCACACGGCAC 1 FAS2 ( 567) TTCACATGCTAC 1 OPI3 ( 340) TTCAGATCGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5523 bayes= 9.62205 E= 2.0e-001 -945 -945 -945 162 -945 -945 -945 162 -945 251 -945 -945 140 -945 -945 -118 -945 229 -30 -945 162 -945 -945 -945 -945 -30 -945 140 -945 -30 229 -945 -945 170 129 -945 -945 229 -945 -118 -18 -30 129 -118 -945 251 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 2.0e-001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.857143 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.857143 0.000000 0.142857 0.285714 0.142857 0.428571 0.142857 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- Time 20.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 10 sites = 7 llr = 81 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::1:::9:6: pos.-specific C :a:::a:911 probability G 3:1aa:1:19 matrix T 7:7::::11: bits 2.5 * *** 2.3 * *** 2.0 * *** * 1.8 * *** * * Information 1.5 * *** * * content 1.3 * ***** * (16.7 bits) 1.0 ** ***** * 0.8 ** ***** * 0.5 ******** * 0.3 ********** 0.0 ---------- Multilevel TCTGGCACAG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- OPI3 - 186 3.24e-07 GAAAACCAGA TCTGGCACAG ACCGTTGTCA ACC1 + 232 3.24e-07 CCAGTCGTAT TCTGGCACAG TATAGCCTAG CHO1 - 559 3.24e-07 ATATTCAGTG TCTGGCACAG AAGTCTGCAC INO1 - 283 5.29e-06 ACGGTCTACG GCGGGCGCAG TCGCATGTCT FAS1 + 44 6.25e-06 TACACGAGGT GCAGGCACGG TTCACTACTC FAS2 - 185 8.48e-06 TTCTTGCTTT TCTGGCACTC TTGACGGCTT CHO2 - 413 8.48e-06 TTTTGCCGTT TCTGGCATCG CCGTTCATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- OPI3 3.2e-07 185_[-2]_605 ACC1 3.2e-07 231_[+2]_559 CHO1 3.2e-07 558_[-2]_232 INO1 5.3e-06 282_[-2]_508 FAS1 6.3e-06 43_[+2]_747 FAS2 8.5e-06 184_[-2]_606 CHO2 8.5e-06 412_[-2]_378 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=10 seqs=7 OPI3 ( 186) TCTGGCACAG 1 ACC1 ( 232) TCTGGCACAG 1 CHO1 ( 559) TCTGGCACAG 1 INO1 ( 283) GCGGGCGCAG 1 FAS1 ( 44) GCAGGCACGG 1 FAS2 ( 185) TCTGGCACTC 1 CHO2 ( 413) TCTGGCATCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 5537 bayes= 9.62571 E= 1.1e+002 -945 -945 70 114 -945 251 -945 -945 -118 -945 -30 114 -945 -945 251 -945 -945 -945 251 -945 -945 251 -945 -945 140 -945 -30 -945 -945 229 -945 -118 82 -30 -30 -118 -945 -30 229 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 1.1e+002 0.000000 0.000000 0.285714 0.714286 0.000000 1.000000 0.000000 0.000000 0.142857 0.000000 0.142857 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.142857 0.571429 0.142857 0.142857 0.142857 0.000000 0.142857 0.857143 0.000000 -------------------------------------------------------------------------------- Time 41.19 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO1 5.44e-06 152_[+2(1.10e-05)]_396_[-2(3.24e-07)]_42_[+1(4.23e-07)]_17_[+1(1.23e-05)]_149 CHO2 6.96e-05 353_[+1(2.52e-07)]_47_[-2(8.48e-06)]_378 FAS1 4.61e-06 43_[+2(6.25e-06)]_41_[+1(1.85e-08)]_694 FAS2 2.34e-04 184_[-2(8.48e-06)]_372_[+1(9.43e-07)]_222 ACC1 2.09e-06 82_[+1(1.52e-07)]_137_[+2(3.24e-07)]_559 INO1 3.95e-06 282_[-2(5.29e-06)]_327_[-1(1.85e-08)]_55_[+1(7.55e-06)]_102 OPI3 3.70e-05 185_[-2(3.24e-07)]_144_[+1(3.32e-06)]_449 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: pmgm2 ********************************************************************************