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 (2001) Applications of generalized pair hidden Markov models to alignment and gene finding problems. In: Proceedings of the fifth annual international conference on Computational biology (RECOMB '01). ACM , New York, NY, pp. 241-248. ISBN 1-58113-353-7. https://resolver.caltech.edu/CaltechAUTHORS:20170309-084730577

Full text is not posted in this repository. Consult Related URLs below.

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20170309-084730577

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:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1145/369133.369227DOIArticle
http://dl.acm.org/citation.cfm?id=369133.369227&coll=portal&dl=ACMPublisherArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2001 ACM. 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
Record Number:CaltechAUTHORS:20170309-084730577
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170309-084730577
Official Citation:Lior Pachter, Marina Alexandersson, and Simon Cawley. 2001. Applications of generalized pair hidden Markov models to alignment and gene finding problems. In Proceedings of the fifth annual international conference on Computational biology (RECOMB '01). ACM, New York, NY, USA, 241-248. DOI=http://dx.doi.org/10.1145/369133.369227
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74958
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:09 Mar 2017 17:00
Last Modified:24 Feb 2020 10:30

Repository Staff Only: item control page