A probabilistic framework for inferring ancestral genomic orders

Jian Ma

doi:10.1109/BIBM.2010.5706559

A probabilistic framework for inferring ancestral genomic orders

Jian Ma

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

We introduce a probabilistic framework for inferring contiguous ancestral regions. Our previous work, the inferCARs algorithm, is a method based on adjacencies between synteny blocks. However, the local parsimony procedure has the limitation that it ignores many adjacencies that are potentially possible to exist in the ancestors. In this paper, we introduce a probabilistic method for reconstructing ancestral orders. The essential part of this method is to predict the posterior probability of an adjacency occurring in the ancestor based on an extended Jukes-Cantor model for breakpoints. We implemented a program called inferCARsPro to reconstruct contiguous ancestral regions. Both simulation and real data application results are discussed.

Original language	English (US)
Title of host publication	Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Pages	179-184
Number of pages	6
DOIs	https://doi.org/10.1109/BIBM.2010.5706559
State	Published - 2010
Externally published	Yes
Event	2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 - Hong Kong, China Duration: Dec 18 2010 → Dec 21 2010

Publication series

Name	Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Other

Other	2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Country/Territory	China
City	Hong Kong
Period	12/18/10 → 12/21/10

Keywords

Ancestral genome reconstruction
Comparative genomics

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics

Online availability

10.1109/BIBM.2010.5706559

Library availability

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A probabilistic framework for inferring ancestral genomic orders. / Ma, Jian.
Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010. 2010. p. 179-184 5706559 (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Ma, J 2010, A probabilistic framework for inferring ancestral genomic orders. in Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010., 5706559, Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, pp. 179-184, 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, Hong Kong, China, 12/18/10. https://doi.org/10.1109/BIBM.2010.5706559

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A probabilistic framework for inferring ancestral genomic orders

Abstract

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Other

Keywords

ASJC Scopus subject areas

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