******************************************************************************** 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= 3_short.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ecaidB_-_Ada_activator 1.0000 13 ecalkA_-_Ada_activator 1.0000 13 ecada_extraction 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 3_short.fasta -dna -oc . -nostatus -time 7200 -maxsize 60000 -mod zoops -nmotifs 1 -minw 13 -maxw 50 model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 13 maxw= 13 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 3 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= 39 N= 3 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.513 C 0.103 G 0.154 T 0.231 Background letter frequencies (from dataset with add-one prior applied): A 0.488 C 0.116 G 0.163 T 0.233 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 3 llr = 31 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A aa:333737::aa pos.-specific C ::::::::3:a:: probability G :::3:3:3:a::: matrix T ::a37333::::: bits 3.1 * 2.8 * 2.5 ** 2.2 * ** Relative 1.9 * ** Entropy 1.6 * ** (15.1 bits) 1.2 * ** 0.9 *** * ***** 0.6 *** * * ***** 0.3 ************* 0.0 ------------- Multilevel AATATAAAAGCAA consensus GAGTGC sequence T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- ecaidB_-_Ada_activator 1 2.09e-06 . AATGTTTTAGCAA ecada_extraction 1 1.54e-05 . AATTAAAGCGCAA ecalkA_-_Ada_activator 1 1.54e-05 . AATATGAAAGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ecaidB_-_Ada_activator 2.1e-06 [+1] ecada_extraction 1.5e-05 [+1] ecalkA_-_Ada_activator 1.5e-05 [+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=3 ecaidB_-_Ada_activator ( 1) AATGTTTTAGCAA 1 ecada_extraction ( 1) AATTAAAGCGCAA 1 ecalkA_-_Ada_activator ( 1) AATATGAAAGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 3 bayes= -1.45943 E= 1.3e-002 103 -823 -823 -823 103 -823 -823 -823 -823 -823 -823 210 -55 -823 103 52 -55 -823 -823 152 -55 -823 103 52 45 -823 -823 52 -55 -823 103 52 45 152 -823 -823 -823 -823 261 -823 -823 310 -823 -823 103 -823 -823 -823 103 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 3 E= 1.3e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.333333 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.333333 0.666667 0.333333 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 -------------------------------------------------------------------------------- AAT[AGT][TA][AGT][AT][AGT][AC]GCAA -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- ecaidB_-_Ada_activator 2.09e-06 [+1(2.09e-06)] ecalkA_-_Ada_activator 1.54e-05 [+1(1.54e-05)] ecada_extraction 1.54e-05 [+1(1.54e-05)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: sten-0-1.local ******************************************************************************** ZadzwońWyslij SMSDodaj do Skype'aMusisz mieć środki na koncie Skype Bezpłatnie przez Skype'a