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Cited by 243

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

Open access
Salmon-Divon, Mali, Dvinge, Heidi, Tammoja, Kairi, Bertone, Paul·2010·BMC Bioinformatics
DOI 10.1186/1471-2105-11-415
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Abstract

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 genomic sequences encompassing the computed subpeak summits, and identify positional features of interest such as intersection with exon/intron gene components, proximity to up- or downstream transcriptional start sites and cis-regulatory elements. The software can be configured to run either as a pipeline component for high-throughput analyses, or as a cross-platform desktop application with an intuitive user interface. Conclusions: PeakAnalyzer comprises a number of utilities essential for ChIP-seq and ChIP-chip data analysis. High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. Source code in C++ and Java is provided, as are native binaries for Linux, Mac OS X and Windows systems.

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Research works printed but not linked: 24

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Cited by

Metadata

Authors
Salmon-Divon, M., Dvinge, H., Tammoja, K., & Bertone, P.
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2010-08-06
Volume
11
Issue
1
Pages
415-415
ISSN
1471-2105 (ISSN-L)
DOI
10.1186/1471-2105-11-415
OpenAlex
W2055303035
Cited by
243
References
4
FWCI
6.14
Type
journal article
Language
en
Open access
gold

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