******************************************************************************** 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/exd_factor_binding_sites_sequences.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ exd_chr2L_2446334_244634 1.0000 9 exd_chr2L_2446266_244627 1.0000 9 exd_chr3R_2613153_261317 1.0000 21 exd_chr2L_2446120_244613 1.0000 11 exd_chr2L_2446086_244609 1.0000 11 exd_chr2L_2446190_244619 1.0000 9 ******************************************************************************** ******************************************************************************** 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/exd_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= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 6 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= 6 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.357 C 0.143 G 0.143 T 0.357 Background letter frequencies (from dataset with add-one prior applied): A 0.351 C 0.149 G 0.149 T 0.351 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 6 llr = 26 E-value = 9.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a2:5a5 pos.-specific C ::8::: probability G :3:3:: matrix T :522:5 bits 2.8 2.5 2.2 1.9 * Information 1.7 * content 1.4 * * * (6.3 bits) 1.1 * * * 0.8 * * * 0.6 ****** 0.3 ****** 0.0 ------ Multilevel ATCAAA consensus G G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------ exd_chr2L_2446086_244609 - 3 1.63e-03 GAA ATCGAA AT exd_chr2L_2446334_244634 - 4 1.63e-03 . ATCGAT AAA exd_chr2L_2446190_244619 + 1 3.22e-03 . ATCAAT TAG exd_chr3R_2613153_261317 + 5 4.57e-03 TTGG AGCTAA TGCGTGGCAA exd_chr2L_2446120_244613 - 3 7.75e-03 TAA AACAAA CA exd_chr2L_2446266_244627 + 1 1.16e-02 . AGTAAT AAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- exd_chr2L_2446086_244609 0.0016 2_[-1]_3 exd_chr2L_2446334_244634 0.0016 3_[-1] exd_chr2L_2446190_244619 0.0032 [+1]_3 exd_chr3R_2613153_261317 0.0046 4_[+1]_11 exd_chr2L_2446120_244613 0.0078 2_[-1]_3 exd_chr2L_2446266_244627 0.012 [+1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=6 exd_chr2L_2446086_244609 ( 3) ATCGAA 1 exd_chr2L_2446334_244634 ( 4) ATCGAT 1 exd_chr2L_2446190_244619 ( 1) ATCAAT 1 exd_chr3R_2613153_261317 ( 5) AGCTAA 1 exd_chr2L_2446120_244613 ( 3) AACAAA 1 exd_chr2L_2446266_244627 ( 1) AGTAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 40 bayes= 2.5025 E= 9.6e+001 151 -923 -923 -923 -107 -923 116 51 -923 249 -923 -107 51 -923 116 -107 151 -923 -923 -923 51 -923 -923 51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 6 E= 9.6e+001 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.333333 0.500000 0.000000 0.833333 0.000000 0.166667 0.500000 0.000000 0.333333 0.166667 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[TG]C[AG]A[AT] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- exd_chr2L_2446334_244634 1.30e-02 9 exd_chr2L_2446266_244627 8.92e-02 9 exd_chr3R_2613153_261317 1.36e-01 21 exd_chr2L_2446120_244613 8.92e-02 11 exd_chr2L_2446086_244609 1.94e-02 11 exd_chr2L_2446190_244619 2.55e-02 9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: jturatsi.scmbb.ulb.ac.be ********************************************************************************