******************************************************************************** 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/grh_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ grh_chr3R_12560254_12560 1.0000 16 grh_chr3R_2688282_268829 1.0000 15 grh_chr2L_19116290_19116 1.0000 13 grh_chr2L_2456665_245667 1.0000 7 grh_chr3R_26677842_26677 1.0000 23 grh_chr2R_15777573_15777 1.0000 20 grh_chr3R_2581252_258127 1.0000 20 grh_chr3R_2688374_268838 1.0000 16 grh_chr3R_2688329_268836 1.0000 35 grh_chr3R_2688252_268826 1.0000 16 ******************************************************************************** ******************************************************************************** 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/grh_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= 181 N= 10 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.232 G 0.232 T 0.268 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 = 5 llr = 50 E-value = 2.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A aaaa2:a: pos.-specific C ::::8a:: probability G :::::::8 matrix T :::::::2 bits 2.1 * 1.9 **** ** 1.7 **** ** 1.5 **** ** Information 1.3 ******** content 1.1 ******** (14.3 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAACCAG consensus A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- grh_chr3R_2688374_268838 + 5 1.72e-05 CTGC AAAACCAG AAAG grh_chr2R_15777573_15777 + 4 1.72e-05 ATC AAAACCAG TTGGCAGGC grh_chr3R_12560254_12560 + 5 1.72e-05 GCTC AAAACCAG ATTG grh_chr3R_2688329_268836 - 5 5.69e-05 AGTAGGATAT AAAACCAT CCGA grh_chr3R_2688282_268829 - 6 5.69e-05 GG AAAAACAG CTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- grh_chr3R_2688374_268838 1.7e-05 4_[+1]_4 grh_chr2R_15777573_15777 1.7e-05 3_[+1]_9 grh_chr3R_12560254_12560 1.7e-05 4_[+1]_4 grh_chr3R_2688329_268836 5.7e-05 4_[-1]_23 grh_chr3R_2688282_268829 5.7e-05 5_[-1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=5 grh_chr3R_2688374_268838 ( 5) AAAACCAG 1 grh_chr2R_15777573_15777 ( 4) AAAACCAG 1 grh_chr3R_12560254_12560 ( 5) AAAACCAG 1 grh_chr3R_2688329_268836 ( 5) AAAACCAT 1 grh_chr3R_2688282_268829 ( 6) AAAAACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 111 bayes= 3.80735 E= 2.8e-001 190 -897 -897 -897 190 -897 -897 -897 190 -897 -897 -897 190 -897 -897 -897 -42 178 -897 -897 -897 210 -897 -897 190 -897 -897 -897 -897 -897 178 -42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 2.8e-001 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AAAA[CA]CA[GT] -------------------------------------------------------------------------------- Time 0.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- grh_chr3R_12560254_12560 3.10e-04 4_[+1(1.72e-05)]_4 grh_chr3R_2688282_268829 9.10e-04 5_[-1(5.69e-05)]_2 grh_chr2L_19116290_19116 2.56e-01 13 grh_chr2L_2456665_245667 1.00e+00 7 grh_chr3R_26677842_26677 1.80e-01 23 grh_chr2R_15777573_15777 4.48e-04 3_[+1(1.72e-05)]_9 grh_chr3R_2581252_258127 5.71e-01 20 grh_chr3R_2688374_268838 3.10e-04 4_[+1(1.72e-05)]_4 grh_chr3R_2688329_268836 3.18e-03 4_[-1(5.69e-05)]_23 grh_chr3R_2688252_268826 8.23e-01 16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************