Sequential modeling for identifying CpG island locations in human genome

Nilanjan Dasgupta, Simon Lin, Lawrence Carin

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

We consider several sequential processing algorithms for identifying genes in human DNA, based on detecting CpG ("C proceeds G") islands. The algorithms are designed to capture the underlying statistical structure in a DNA sequence. Sequential processing using a Markov model and a hidden Markov model are shown to identify most CpG islands in annotated (marked) DNA subsequences available from publicly available DNA datasets. We also consider a wavelet-based hidden Markov tree (HMT). In the context of the HMT, we address design of adaptive wavelets matched to CpG islands, this accomplished via lifting and genetic-algorithm optimization.
Original languageEnglish (US)
Pages (from-to)407-409
Number of pages3
JournalIEEE Signal Processing Letters
Volume9
Issue number12
DOIs
StatePublished - Dec 1 2002
Externally publishedYes

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