http://dx.doi.org/10.1186/1479-7364-5-2-117">
 

Document Type

Journal Article

Department/Unit

Department of Mathematics

Title

A short survey of computational analysis methods in analysing ChIP-seq data

Language

English

Abstract

Chromatin immunoprecipitation followed by massively parallel next-generation sequencing (ChIP-seq) is a valuable experimental strategy for assaying protein-DNA interaction over the whole genome. Many computational tools have been designed to find the peaks of the signals corresponding to protein binding sites. In this paper, three computational methods, ChIP-seq processing pipeline (spp), PeakSeq and CisGenome, used in ChIP-seq data analysis are reviewed. There is also a comparison of how they agree and disagree on finding peaks using the publically available Signal Transducers and Activators of Transcription protein 1 (STAT1) and RNA polymerase II (PolII) datasets with corresponding negative controls. © HENRY STEWART PUBLICATIONS.

Keywords

Bioinformatics, CHIP-Seq analysis, Comparative analysis, Next-generation sequencing

Publication Date

2011

Source Publication Title

Human Genomics

Volume

5

Start Page

117

End Page

123

Publisher

BioMed Central

ISSN (print)

14739542

ISSN (electronic)

14797364

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