Suite for Computational identification Of Promoter Elements

[…] was used to identify potential ier3 binding motifs. minimal motif width from 6 to 4 and maximum motif width from 6–10, 14 and 50 were tested. the ier3 binding motif was confirmed by chipmotifs [], suite for computational identification of promoter elements (scope) [] and discovering ranked imbalanced motifs using suffix trees (drimust) [] and then analyzed by find individual motif occurrences […]

[…] reported except in circumstances where no biological process was enriched with the gene set, in which case, go terms for components were highlighted. a p-value cutoff was set to 0.05 (see )., the suite for computational identification of promoter elements, “scope” motif finder ( http://genie.dartmouth.edu/scope/) was used to predict candidate promoter motifs in this study. the scope motif […]

[…] processes as described in the gene ontology (go) database using david 6.7 [] and default parameters., we searched for conserved motifs in the promoter region of the zygotic mrnas using scope (suite for computational identification of promoter elements), which is a parameter-free program designed to identify cis sequences in a set of co-regulated mrnas (http://genie.dartmouth.edu/scope/) […]

[…] sites used jaspar . phylogenetic conservation employed the whole genome rvista browser . est mapping was according to the ucsc genome browser database . predicted promoter consensus sequences used suite for computational identification of promoter elements (scope) . genomes of reference were drosophila bdgp r5/dm3 and human grch37releases., we thank j. l. gómez-skarmeta and a. fernández-miñán […]

[…] bp around peak summits in sfl1p or sfl2p data sets were extracted using the extract genomic dna tool version 2.2.2. the resulting sequences were used as input for motif discovery using the scope (suite for computational identification of promoter elements, version 2.1.0) program (http://genie.dartmouth.edu/scope/) or the regulatory sequence analysis tools ([rsat] http://rsat.ulb.ac.be/rsat/) […]