A probabilistic framework for inferring ancestral genomic orders

Jian Ma

Research output: Chapter in Book/Report/Conference proceedingConference 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 languageEnglish (US)
Title of host publicationProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Pages179-184
Number of pages6
DOIs
StatePublished - Dec 1 2010
Event2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 - Hong Kong, China
Duration: Dec 18 2010Dec 21 2010

Publication series

NameProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Other

Other2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
CountryChina
CityHong Kong
Period12/18/1012/21/10

Keywords

  • Ancestral genome reconstruction
  • Comparative genomics

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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  • Cite this

    Ma, J. (2010). A probabilistic framework for inferring ancestral genomic orders. In Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 (pp. 179-184). [5706559] (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010). https://doi.org/10.1109/BIBM.2010.5706559