title: biomvRhsmm: genomic segmentation with hidden semi-Markov model.
abstract: High-throughput technologies like tiling array and next-generation sequencing (NGS) generate continuous homogeneous segments or signal peaks in the genome that represent transcripts and transcript variants (transcript mapping and quantification), regions of deletion and amplification (copy number variation), or regions characterized by particular common features like chromatin state or DNA methylation ratio (epigenetic modifications). However, the volume and output of data produced by these technologies present challenges in analysis. Here, a hidden semi-Markov model (HSMM) is implemented and tailored to handle multiple genomic profile, to better facilitate genome annotation by assisting in the detection of transcripts, regulatory regions, and copy number variation by holistic microarray or NGS. With support for various data distributions, instead of limiting itself to one specific application, the proposed hidden semi-Markov model is designed to allow modeling options to accommodate different types of genomic data and to serve as a general segmentation engine. By incorporating genomic positions into the sojourn distribution of HSMM, with optional prior learning using annotation or previous studies, the modeling output is more biologically sensible. The proposed model has been compared with several other state-of-the-art segmentation models through simulation benchmarking, which shows that our efficient implementation achieves comparable or better sensitivity and specificity in genomic segmentation.
authors.affiliation: Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany.
authors.forename: Yang
authors.identifier: 0000-0002-5707-513X
authors.initials: Y
authors.lastname: Du
authors.affiliation: Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany.
authors.forename: Eduard
authors.initials: E
authors.lastname: Murani
authors.affiliation: Research Group Functional Genomics, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany.
authors.forename: Siriluck
authors.initials: S
authors.lastname: Ponsuksili
authors.affiliation: Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany.
authors.forename: Klaus
authors.identifier: 0000-0002-9523-6790
authors.initials: K
authors.lastname: Wimmers
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D056915:DNA Copy Number Variations / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008390:Markov Chains; D015233:Models, Statistical