Hill Finder
Detection of Proximal RNA Binding Sites in HITS Data
High-throughput sequencing has been widely used to find novel protein-binding RNAs, utilizing methods such as CLIP-Seq and Genomic SELEX. Typical analyses of the high-throughput data employ the use of a histogram of the aligned read count per base, the intensity of which indicates, for a specific region of an RNA, the underlying sequence's relative occurrence of binding events in the experiment. This technique can, however, obscure the precise locations of binding sites in close proximity to each other, which would be found when analyzing high-throughput data for enzymes whose activity require multiple RNA binding sites, as well as for overlapping distinct ncRNA loci derived from processing events. ...