******************************************************************************** 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/abd-A_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ abd-A_chr3R_2759787_2759 1.0000 21 abd-A_chr3R_2759180_2759 1.0000 21 abd-A_chr3R_2759820_2759 1.0000 10 abd-A_chr3R_2759514_2759 1.0000 15 abd-A_chr3R_2759290_2759 1.0000 24 abd-A_chr2L_21840884_218 1.0000 20 abd-A_chr2L_21840626_218 1.0000 16 abd-A_chr3R_2759096_2759 1.0000 22 abd-A_chr3R_2759274_2759 1.0000 11 abd-A_chr2L_2446323_2446 1.0000 9 abd-A_chr2L_2446281_2446 1.0000 6 abd-A_chr3R_2760512_2760 1.0000 17 abd-A_chr2L_2445914_2445 1.0000 16 abd-A_chr3R_2760074_2760 1.0000 20 abd-A_chr2L_2445884_2445 1.0000 10 abd-A_chr2L_21840736_218 1.0000 13 abd-A_chr3R_2760146_2760 1.0000 46 abd-A_chr3R_2758978_2758 1.0000 21 abd-A_chr3R_2759541_2759 1.0000 12 abd-A_chr3R_2759484_2759 1.0000 17 abd-A_chr3R_2759395_2759 1.0000 28 abd-A_chr3R_2758951_2758 1.0000 18 abd-A_chr2L_21840808_218 1.0000 21 abd-A_chr2R_20311248_203 1.0000 19 abd-A_chr3R_2760544_2760 1.0000 20 abd-A_chr3R_2758919_2758 1.0000 22 abd-A_chr3R_2759631_2759 1.0000 31 abd-A_chr2L_2446190_2446 1.0000 9 abd-A_chr2L_2446071_2446 1.0000 22 abd-A_chr3R_2758853_2758 1.0000 18 abd-A_chr3R_2760609_2760 1.0000 16 abd-A_chr3R_2759464_2759 1.0000 19 abd-A_chr2L_2446259_2446 1.0000 17 abd-A_chr2L_2446291_2446 1.0000 6 abd-A_chr3R_2759001_2759 1.0000 16 abd-A_chr3R_2760472_2760 1.0000 18 abd-A_chr3R_2759526_2759 1.0000 7 abd-A_chr3R_2760341_2760 1.0000 25 abd-A_chr3R_2760273_2760 1.0000 13 abd-A_chr3R_2759244_2759 1.0000 10 ******************************************************************************** ******************************************************************************** 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/abd-A_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= 40 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 702 N= 40 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.372 C 0.128 G 0.128 T 0.372 Background letter frequencies (from dataset with add-one prior applied): A 0.371 C 0.129 G 0.129 T 0.371 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 6 llr = 57 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::2::8 pos.-specific C ::272:a2 probability G :a8::3:: matrix T a::377:: bits 3.0 * * 2.7 * * 2.4 ** * 2.1 ** * Information 1.8 ** * content 1.5 **** * (13.7 bits) 1.2 **** * 0.9 **** *** 0.6 **** *** 0.3 ******** 0.0 -------- Multilevel TGGCTTCA consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- abd-A_chr3R_2760146_2760 - 29 7.69e-06 TTTAGATTTA TGGCTTCA CGCAATTAGT abd-A_chr3R_2760074_2760 + 5 7.69e-06 GGTA TGGCTTCA TTACGCCG abd-A_chr2L_2446071_2446 + 7 1.22e-05 CCCATT TGGCTTCC CATTTCGA abd-A_chr3R_2759631_2759 - 9 1.46e-05 TATATATTCA TGGCAGCA ATTATCGG abd-A_chr2L_2445914_2445 - 5 5.09e-05 GTAA TGGTCGCA TTAC abd-A_chr3R_2759484_2759 - 1 1.24e-04 TTTCTTTAT TGCTTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- abd-A_chr3R_2760146_2760 7.7e-06 28_[-1]_10 abd-A_chr3R_2760074_2760 7.7e-06 4_[+1]_8 abd-A_chr2L_2446071_2446 1.2e-05 6_[+1]_8 abd-A_chr3R_2759631_2759 1.5e-05 8_[-1]_15 abd-A_chr2L_2445914_2445 5.1e-05 4_[-1]_4 abd-A_chr3R_2759484_2759 0.00012 [-1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=6 abd-A_chr3R_2760146_2760 ( 29) TGGCTTCA 1 abd-A_chr3R_2760074_2760 ( 5) TGGCTTCA 1 abd-A_chr2L_2446071_2446 ( 7) TGGCTTCC 1 abd-A_chr3R_2759631_2759 ( 9) TGGCAGCA 1 abd-A_chr2L_2445914_2445 ( 5) TGGTCGCA 1 abd-A_chr3R_2759484_2759 ( 1) TGCTTTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 422 bayes= 6.56847 E= 1.1e+003 -923 -923 -923 143 -923 -923 295 -923 -923 37 269 -923 -923 237 -923 -15 -115 37 -923 84 -923 -923 137 84 -923 295 -923 -923 117 37 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 1.1e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.666667 0.000000 0.333333 0.166667 0.166667 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TGG[CT]T[TG]CA -------------------------------------------------------------------------------- Time 0.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- abd-A_chr3R_2759787_2759 9.16e-01 21 abd-A_chr3R_2759180_2759 9.51e-01 21 abd-A_chr3R_2759820_2759 5.59e-01 10 abd-A_chr3R_2759514_2759 6.98e-01 15 abd-A_chr3R_2759290_2759 6.18e-01 24 abd-A_chr2L_21840884_218 9.60e-01 20 abd-A_chr2L_21840626_218 7.40e-01 16 abd-A_chr3R_2759096_2759 4.18e-01 22 abd-A_chr3R_2759274_2759 9.99e-01 11 abd-A_chr2L_2446323_2446 8.32e-02 9 abd-A_chr2L_2446281_2446 1.00e+00 6 abd-A_chr3R_2760512_2760 9.16e-01 17 abd-A_chr2L_2445914_2445 9.17e-04 4_[-1(5.09e-05)]_4 abd-A_chr3R_2760074_2760 2.00e-04 4_[+1(7.69e-06)]_8 abd-A_chr2L_2445884_2445 5.13e-02 10 abd-A_chr2L_21840736_218 7.88e-01 13 abd-A_chr3R_2760146_2760 5.99e-04 28_[-1(7.69e-06)]_10 abd-A_chr3R_2758978_2758 6.61e-01 21 abd-A_chr3R_2759541_2759 7.09e-01 12 abd-A_chr3R_2759484_2759 2.48e-03 17 abd-A_chr3R_2759395_2759 4.45e-01 28 abd-A_chr3R_2758951_2758 4.91e-01 18 abd-A_chr2L_21840808_218 8.42e-01 21 abd-A_chr2R_20311248_203 7.34e-01 19 abd-A_chr3R_2760544_2760 4.06e-01 20 abd-A_chr3R_2758919_2758 5.86e-01 22 abd-A_chr3R_2759631_2759 7.02e-04 8_[-1(1.46e-05)]_15 abd-A_chr2L_2446190_2446 7.46e-01 9 abd-A_chr2L_2446071_2446 3.65e-04 6_[+1(1.22e-05)]_8 abd-A_chr3R_2758853_2758 5.01e-01 18 abd-A_chr3R_2760609_2760 3.24e-01 16 abd-A_chr3R_2759464_2759 7.34e-01 19 abd-A_chr2L_2446259_2446 9.25e-01 17 abd-A_chr2L_2446291_2446 1.00e+00 6 abd-A_chr3R_2759001_2759 5.01e-01 16 abd-A_chr3R_2760472_2760 9.60e-01 18 abd-A_chr3R_2759526_2759 1.00e+00 7 abd-A_chr3R_2760341_2760 5.13e-01 25 abd-A_chr3R_2760273_2760 1.55e-01 13 abd-A_chr3R_2759244_2759 9.72e-01 10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************