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
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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 | |||||||||
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| 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. | |||||||||
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| DOI: | 10.1145/369133.369227 | |||||||||
| 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: | 15 Nov 2021 16:29 |
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