Sentence examples for motif search program from inspiring English sources

We searched for putative ER target sequences within the promoter of the CST6 by using the motif search program [ 25].

We also searched p53- and p73-bound promoters against the JASPAR database [ 46] using the motif search program Cis-eLement OVERrepresentation [ 47] for other over-represented motifs corresponding to 123 curated transcription factor-binding motifs using P value cutoff < 0.001.

When using the motif search program MEME [ 66] with all four promoters that SlMYC1 can activate, one 8 bp motif was identified in the plus or minus (for SlTPS9) orientation: CTAGG(T/A)(A/G G.

Candidate chemoreceptor sequences from the results of TBLASTN were compared with ab initio gene predictions (see Gene annotation section) and verified its functional domain using the MOTIF search program [ 110].

The first method depends on ab initio motif searching based on the supposition that if there are cis-elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented in the associated promoter sequences as conserved motifs that can be identified by using a suitable motif search program.

Note that the definition of the TOP motif allows for variable lengths, which is not examined in typical motif search programs.

The sequence motif search programs MEME (Multiple EM for motif elicitation), MDScan, and Weeder were used [ 80- 83].

Motif search programs were performed for the 70 motifs extracted at Step2-1 and the 4 MafB motifs at Step1-3 witheTFSEARCHandH and TFBIND algorithms, which are libraries of preexisting motifs for transcription factors.

Three motif searching programs have been used for the purpose: MEME [ 22], Weeder [ 23, 24] and AlignACE [ 25].

Moreover, motif-searching programs, too, when run in single or double-stranded modes, report complementary motifs as separate motifs.

Identification of statistically overrepresented motifs was done by using the motif search MEME program [ 22].