******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.9.0 (Release date: Wed Oct 3 11:07:26 EST 2012) 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= Ppmot.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ F1_aidB 1.0000 13 S16_aidB 1.0000 13 GB-1_aidB 1.0000 13 KT2440_aidB 1.0000 13 KT2440_alkA 1.0000 13 F1_alkA 1.0000 13 W619_alkA 1.0000 13 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme Ppmot.fasta -dna -oc . -nostatus -time 7200 -maxsize 60000 -mod zoops -nmotifs 1 -minw 6 -maxw 50 model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 13 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 7 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 91 N= 7 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.308 C 0.198 G 0.275 T 0.220 Background letter frequencies (from dataset with add-one prior applied): A 0.305 C 0.200 G 0.274 T 0.221 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 7 llr = 108 E-value = 6.6e-029 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a6:4:::::::aa pos.-specific C :::1:4::a:a:: probability G ::::a6:a:a::: matrix T :4a4::a:::::: bits 2.3 * * 2.1 * * * * 1.9 * * ***** 1.6 * * * ******* Relative 1.4 * * * ******* Entropy 1.2 * * ********* (22.3 bits) 0.9 *** ********* 0.7 *** ********* 0.5 ************* 0.2 ************* 0.0 ------------- Multilevel AATAGGTGCGCAA consensus T T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- GB-1_aidB 1 6.28e-08 . AATTGGTGCGCAA S16_aidB 1 6.28e-08 . AATTGGTGCGCAA F1_aidB 1 6.28e-08 . AATTGGTGCGCAA W619_alkA 1 9.94e-08 . ATTAGCTGCGCAA F1_alkA 1 9.94e-08 . ATTAGCTGCGCAA KT2440_alkA 1 9.94e-08 . ATTAGCTGCGCAA KT2440_aidB 1 2.06e-07 . AATCGGTGCGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- GB-1_aidB 6.3e-08 [+1] S16_aidB 6.3e-08 [+1] F1_aidB 6.3e-08 [+1] W619_alkA 9.9e-08 [+1] F1_alkA 9.9e-08 [+1] KT2440_alkA 9.9e-08 [+1] KT2440_aidB 2.1e-07 [+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=7 GB-1_aidB ( 1) AATTGGTGCGCAA 1 S16_aidB ( 1) AATTGGTGCGCAA 1 F1_aidB ( 1) AATTGGTGCGCAA 1 W619_alkA ( 1) ATTAGCTGCGCAA 1 F1_alkA ( 1) ATTAGCTGCGCAA 1 KT2440_alkA ( 1) ATTAGCTGCGCAA 1 KT2440_aidB ( 1) AATCGGTGCGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 7 bayes= 0.415037 E= 6.6e-029 171 -945 -945 -945 90 -945 -945 95 -945 -945 -945 218 49 -48 -945 95 -945 -945 187 -945 -945 110 106 -945 -945 -945 -945 218 -945 -945 187 -945 -945 232 -945 -945 -945 -945 187 -945 -945 232 -945 -945 171 -945 -945 -945 171 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 7 E= 6.6e-029 1.000000 0.000000 0.000000 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 0.000000 0.000000 1.000000 0.428571 0.142857 0.000000 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[AT]T[AT]G[GC]TGCGCAA -------------------------------------------------------------------------------- Time 0.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- F1_aidB 6.28e-08 [+1(6.28e-08)] S16_aidB 6.28e-08 [+1(6.28e-08)] GB-1_aidB 6.28e-08 [+1(6.28e-08)] KT2440_aidB 2.06e-07 [+1(2.06e-07)] KT2440_alkA 9.94e-08 [+1(9.94e-08)] F1_alkA 9.94e-08 [+1(9.94e-08)] W619_alkA 9.94e-08 [+1(9.94e-08)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: sten-0-4.local ******************************************************************************** ZadzwońWyslij SMSDodaj do Skype'aMusisz mieć środki na koncie Skype Bezpłatnie przez Skype'a