Article

Applications of generalized pair hidden Markov models to alignment and gene finding problems

Authors:

Marina Alexandersson,

Simon CawleyAuthors Info & Claims

RECOMB '01: Proceedings of the fifth annual international conference on Computational biology

Pages 241 - 248

https://doi.org/10.1145/369133.369227

Published: 22 April 2001 Publication History

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.

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Cited By

Aliakbarpour HKhoshhal KQuintas JMekhnacha KRos JAndersson MDias J(2011)HMM-Based Abnormal Behaviour Detection Using Heterogeneous Sensor NetworkTechnological Innovation for Sustainability10.1007/978-3-642-19170-1_30(277-285)Online publication date: 2011
https://doi.org/10.1007/978-3-642-19170-1_30
Lifshits YMozes SWeimann OZiv-Ukelson M(2009)Speeding Up HMM Decoding and Training by Exploiting Sequence RepetitionsAlgorithmica10.1007/s00453-007-9128-054:3(379-399)Online publication date: 1-May-2009
https://dl.acm.org/doi/10.1007/s00453-007-9128-0
Gao DReiter MSong D(2006)Behavioral distance measurement using hidden markov modelsProceedings of the 9th international conference on Recent Advances in Intrusion Detection10.1007/11856214_2(19-40)Online publication date: 20-Sep-2006
https://dl.acm.org/doi/10.1007/11856214_2
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Index Terms

Applications of generalized pair hidden Markov models to alignment and gene finding problems
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis
      1. Model verification and validation
    2. Simulation types and techniques

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cover image ACM Conferences

RECOMB '01: Proceedings of the fifth annual international conference on Computational biology

April 2001

316 pages

ISBN:1581133537

DOI:10.1145/369133

Chairman:
Thomas Lengauer
German National Research Center for Information Technology, Germany

Copyright © 2001 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 22 April 2001

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RECOMB01: The Fifth Annual International Conference on Computational Molecular Biology

April 22 - 25, 2001

Quebec, Montreal, Canada

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RECOMB '01 Paper Acceptance Rate 35 of 128 submissions, 27%;

Overall Acceptance Rate 148 of 538 submissions, 28%

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Cited By

Aliakbarpour HKhoshhal KQuintas JMekhnacha KRos JAndersson MDias J(2011)HMM-Based Abnormal Behaviour Detection Using Heterogeneous Sensor NetworkTechnological Innovation for Sustainability10.1007/978-3-642-19170-1_30(277-285)Online publication date: 2011
https://doi.org/10.1007/978-3-642-19170-1_30
Lifshits YMozes SWeimann OZiv-Ukelson M(2009)Speeding Up HMM Decoding and Training by Exploiting Sequence RepetitionsAlgorithmica10.1007/s00453-007-9128-054:3(379-399)Online publication date: 1-May-2009
https://dl.acm.org/doi/10.1007/s00453-007-9128-0
Gao DReiter MSong D(2006)Behavioral distance measurement using hidden markov modelsProceedings of the 9th international conference on Recent Advances in Intrusion Detection10.1007/11856214_2(19-40)Online publication date: 20-Sep-2006
https://dl.acm.org/doi/10.1007/11856214_2
Bonner ALiu H(2004)Comparison of discrimination methods for peptide classification in tandem mass spectrometryIGARSS 2004. 2004 IEEE International Geoscience and Remote Sensing (IEEE Cat. No.04CH37612)10.1109/CIBCB.2004.1393949(160-167)Online publication date: 2004
https://doi.org/10.1109/CIBCB.2004.1393949
Alexandersson MCawley SPachter L(2003)SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov ModelGenome Research10.1101/gr.42420313:3(496-502)Online publication date: 12-Feb-2003
https://doi.org/10.1101/gr.424203
Pedersen CScharling T(2002)Comparative Methods for Gene Structure Prediction in Homologous SequencesAlgorithms in Bioinformatics10.1007/3-540-45784-4_17(220-234)Online publication date: 10-Oct-2002
https://doi.org/10.1007/3-540-45784-4_17

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