PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

Background: Functional genomic studies involving high-throughput sequencing and tiling array applications, such as ChIP-seq and ChIP-chip, generate large numbers of experimentally-derived signal peaks across the genome under study. In analyzing these loci to determine their potential regulatory functions, areas of signal enrichment must be considered relative to proximal genes and regulatory elements annotated throughout the target genome Regions of chromatin association by transcriptional regulators should be distinguished as individual binding sites in order to enhance downstream analyses, such as the identification of known and novel consensus motifs. Results: PeakAnalyzer is a set of high-performance utilities for the automated processing of experimentally-derived peak regions and annotation of genomic loci. The programs can accurately subdivide multimodal regions of signal enrichment into distinct subpeaks corresponding to binding sites or chromatin modifications, retrieve genomi...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Mali Salmon-Divon, Heidi Dvinge, Kairi Tammoja, Paul Bertone
• Keywords: Binding Sites, BMCBI 2010, Regulatory Elements, Signal Enrichment