CaltechAUTHORS
  A Caltech Library Service

Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems

Pachter, Lior and Alexandersson, Marina and Cawley, Simon (2002) Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems. Journal of Computational Biology, 9 (2). pp. 389-399. ISSN 1066-5277. https://resolver.caltech.edu/CaltechAUTHORS:20170309-092737635

[img] PDF - Published Version
See Usage Policy.

233Kb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20170309-092737635

Abstract

Hidden Markov models (HMMs) have been successfully applied to a variety of problems in molecular biology, ranging from alignment problems to gene finding and annotation. Alignment problems can be solved with pair HMMs, while gene finding programs rely on generalized HMMs in order to model exon lengths. In this paper, we introduce the generalized pair HMM (GPHMM), which is an extension of both pair and generalized HMMs. We show how GPHMMs, in conjunction with approximate alignments, can be used for cross-species gene finding and describe applications to DNA–cDNA and DNA–protein alignment. GPHMMs provide a unifying and probabilistically sound theory for modeling these problems.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1089/10665270252935520DOIArticle
http://online.liebertpub.com/doi/abs/10.1089/10665270252935520PublisherArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2002 Mary Ann Liebert, Inc. We thank Terry Speed for valuable comments. M.A. was supported by STINT, the Swedish Foundation for International Cooperation in Research and Higher Education.
Funders:
Funding AgencyGrant Number
Swedish Foundation for International Cooperation in Research and Higher Education (STINT)UNSPECIFIED
Subject Keywords:hidden Markov model, alignment, gene �finding, comparative genomics
Issue or Number:2
Record Number:CaltechAUTHORS:20170309-092737635
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170309-092737635
Official Citation:Lior Pachter, Marina Alexandersson, and Simon Cawley. Journal of Computational Biology. July 2004, 9(2): 389-399. doi:10.1089/10665270252935520.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74967
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:10 Mar 2017 04:02
Last Modified:24 Feb 2020 10:30

Repository Staff Only: item control page