HPeak 2.1 – Define Genome-wide ChIP-enriched Peaks in Human Genome

HPeak 2.1


HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites.ChIP-Seq is an important application of the massively parallel sequencing technologies aiming to identify all the locations in the genome where a specific protein binds. While direct counting of the sequencing reads can reveal many such binding sites, it is desirable to develop a statistical sound method to explicitly model the uncertainties involved for better and more interpretable results.



Steve Qin @ the Center for Statistical Genetics




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Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM (2010).
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.
BMC Bioinformatics, 11:369

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