******************************************************************************** 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/srp_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ srp_chr3L_14063443_14063 1.0000 18 srp_chrX_9898915_9898926 1.0000 12 srp_chr2L_14616180_14616 1.0000 14 srp_chr3L_14063390_14063 1.0000 26 ******************************************************************************** ******************************************************************************** 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/srp_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= 4 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 70 N= 4 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.236 G 0.236 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.236 G 0.236 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 4 llr = 26 E-value = 1.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a::3 pos.-specific C 8::3a: probability G :::::8 matrix T 3a:8:: bits 2.1 * 1.9 ** * 1.7 ** * 1.5 ** * Information 1.2 ****** content 1.0 ****** (9.5 bits) 0.8 ****** 0.6 ****** 0.4 ****** 0.2 ****** 0.0 ------ Multilevel CTATCG consensus T C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ srp_chr3L_14063390_14063 + 4 2.42e-04 GGC CTATCG CTTGACTCCC srp_chrX_9898915_9898926 + 2 2.42e-04 G CTATCG ATAGC srp_chr2L_14616180_14616 - 4 4.59e-04 ATTAT CTACCG TTA srp_chr3L_14063443_14063 + 5 1.78e-03 ATGT TTATCA GCCCAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- srp_chr3L_14063390_14063 0.00024 3_[+1]_17 srp_chrX_9898915_9898926 0.00024 1_[+1]_5 srp_chr2L_14616180_14616 0.00046 3_[-1]_5 srp_chr3L_14063443_14063 0.0018 4_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=4 srp_chr3L_14063390_14063 ( 4) CTATCG 1 srp_chrX_9898915_9898926 ( 2) CTATCG 1 srp_chr2L_14616180_14616 ( 4) CTACCG 1 srp_chr3L_14063443_14063 ( 5) TTATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 50 bayes= 4.30986 E= 1.9e+001 -865 166 -865 -8 -865 -865 -865 192 192 -865 -865 -865 -865 8 -865 151 -865 208 -865 -865 -8 -865 166 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 4 E= 1.9e+001 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]TA[TC]C[GA] -------------------------------------------------------------------------------- Time 0.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- srp_chr3L_14063443_14063 4.53e-02 18 srp_chrX_9898915_9898926 3.38e-03 12 srp_chr2L_14616180_14616 8.23e-03 14 srp_chr3L_14063390_14063 1.01e-02 26 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************