NDLI: Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution

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Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution

Content Provider	ACM Digital Library
Author	Berglund, Ann-Charlotte Lagergren, Jens Sennblad, Bengt Arvestad, Lars
Abstract	Gene tree and species tree reconstruction, orthology analysis and reconciliation, are problems important in multigenome-based comparative genomics and biology in general. In the present paper, we advance the frontier of these areas in several respects and provide important computational tools. First, exact algorithms are given for several probabilistic reconciliation problems with respect to the probabilistic gene evolution model, previously developed by the authors. Until now, those problems were solved by MCMC estimation algorithms. Second, we extend the gene evolution model to the gene sequence evolution model, by including sequence evolution. Third, we develop MCMC algorithms for the gene sequence evolution model that, given gene sequence data allows: (1) orthology analysis, reconciliation analysis, and gene tree reconstruction, w.r.t. a species tree, that balances a likely/unlikely reconciliation and a likely/unlikely gene tree and (2) species tree reconstruction that balance a likely/unlikely reconciliation and a likely/unlikely gene trees. These MCMC algorithms take advantage of the exact algorithms for the gene evolution model. We have successfully tested our dynamical programming algorithms on real data for a biogeography problem. The MCMC algorithms perform very well both on synthetic and biological data.
Starting Page	326
Ending Page	335
Page Count	10
File Format	PDF
ISBN	1581137559
DOI	10.1145/974614.974657
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2004-03-27
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Algorithms Orthology Reconciliation Gene tree Bayesian analysis
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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