swMATH ID: 29576
Software Authors: Qin ZS, Yu J, Shen J, et al.
Description: HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. Results: Here we introduce HPeak, a H idden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP-Seq data to identify protein-interacting genomic regions. In contrast to the majority of available ChIP-Seq analysis software packages, HPeak is a model-based approach allowing for rigorous statistical inference. This approach enables HPeak to accurately infer genomic regions enriched with sequence reads by assuming realistic probability distributions, in conjunction with a novel weighting scheme on the sequencing read coverage. Conclusions: Using biologically relevant data collections, we found that HPeak showed a higher prevalence of the expected transcription factor binding motifs in ChIP-enriched sequences relative to the control sequences when compared to other currently available ChIP-Seq analysis approaches. Additionally, in comparison to the ChIP-chip assay, ChIP-Seq provides higher resolution along with improved sensitivity and specificity of binding site detection. Additional file and the HPeak program are freely available at http://www.sph.umich.edu/csg/qin/HPeak.
Homepage: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-369
Related Software: BayesPeak; CLIPZ; COUNT; KEGG; DEGseq; starBase; BSMAP; ROAST; Velvet; ARACHNE; SpliceTrap; DWE; mirTools; miRExpress; TargetSpy; miRNAkey; PatMaN; SeqBuster; ProMiR II; MiRonTop
Cited in: 4 Documents

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