Sentence examples for many binding intervals from inspiring English sources
> Translating sequence reads from each non- melanogaster species to the D. melanogaster genome coordinates and calling binding intervals on the translated data showed that, while differences between species were observed, many binding intervals were conserved across the species.
Given a set of transcription factor binding intervals from a ChIP-seq experiment in BED format (nfkb.bed), we wish to determine how many binding intervals lie within exons, introns or intergenic sequence using a reference gene set from GENCODE (Harrow et al., 2012), in GTF format (hg19.gtf).
In addition, in many cases, multiple binding intervals are annotated to the same target gene, and these are unlikely to be equally functional.
While we recognise that this is a relatively stringent filter and will not include many bona fide Dichaete binding intervals, we contend that focusing on independently verified binding locations will allow us to make more confident inferences about Dichaete function in the embryo.
Our analysis of various CNS pathways suggested Dichaete involvement in many different processes and to elaborate this further we compared our core Dichaete binding intervals with a range of binding data generated by the BDTNP and modENCODE projects.
Additional file 2: Genes annotated to Sox DamID binding intervals.
Similar results were found for binding intervals within FlyLight enhancers.
These binding intervals were used for further analysis.
Genomic features annotated to group B Sox DamID binding intervals.
Two strategies were used to predict Sox binding sites within binding intervals.
For each translated DamID binding interval dataset, the total number of binding intervals overlapping an intron by at least 100 bp, as well as the number of binding intervals overlapping the first intron of a transcript, were counted.
