Sentence examples for motif finding program from inspiring English sources

The motif finding program MEME [ 16] was used to search for enriched motifs in the peaks from our LRH-1 ChIP-seq data set.

When we used the motif finding program MEME [ 16] to search for enriched motifs in the peaks from our LRH-1 ChIP-seq dataset, we found a motif (5'-CCAAGGTCA-3') containing a nuclear receptor half-site (MOTIF 2) and 33% of all input peaks contained at least one LRH-1 motif.

When the phylogenetic footprinting technique is applied to the pooled 50 upstream regions (data not shown) of the operons whose genes are orthologous to those that are regulated by SphR in PCC6803, highly conserved two tandem repeats with a linker are identified in 30 these sequences by our motif finding program CUBIC [ 15] with a cutoff score at p < 0.001.

Motif finding programs including CUBIC [ 37] and BioProspector [ 38], were then applied to predict CRP binding sites in these sequences.

We apply priority and a number of popular motif finding programs to sets of yeast intergenic regions that are reported by ChIP-chip to be bound by particular TFs.

Homopolymers are strongly over-represented in the human genome and therefore are, together with repetitive sequences, frequently picked up by some of the motif finding programs.

Overrepresented sequence motifs identified by BEST were further used if detected by at least 2 out of the 4 motif finding programs.

In our first experiment, we focused on the (15, 4 -motif challenge problem, which is one of the most popular benchmarks for motif finding programs.

Two motif finding programs, MEME [ 25, 43] and BioProspector [ 26], were then applied to these pooled inter-TU regions to identify palindromic 14-mers as putative LexA-binding sites in these sequences according to previous studies [ 16].

To identify conserved sequence motifs for translation starts, ribosome binding sites and promoter regions of B. methanolicus MGA3, the motif-finding program Improbizer [ 23] and the visualization tool WebLogo [ 24] were used with default settings.

In an attempt to determine a physiological role for GlnRII, we used the motif-finding program MEME [ 20] (http://meme.sdsc.edu) to search for a sequence motif within the upstream regions of genes whose transcriptional profile was altered in the glnRII mutant.