Title

PBEAM: A parallel implementation of BEAM for genome-wide inference of epistatic interactions

Authors

Tao Peng, Pufeng Du, Yanda Li

Affiliation

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China

Email

daulyd@tsinghua.edu.cn

Article Type

Software

Date

received February 20, 2009; accepted March 28, 2009; published April 21, 2009

Abstract

The software tool PBEAM provides a parallel implementation of the BEAM, which is the first algorithm for large scale epistatic interaction mapping, including genome-wide studies with hundreds of thousands of markers. BEAM describes markers and their interactions with a Bayesian partitioning model and computes the posterior probability of each marker sets via Markov Chain Monte Carlo (MCMC). PBEAM takes the advantage of simulating multiple Markov chains simultaneously. This design can efficiently reduce ~n-fold execution time in the circumstance of n CPUs. The implementation of PBEAM is based on MPI libraries.

Keywords

genome wide association study, epistatic mapping, Bayesian methods, parallel computing

Availability

PBEAM is available for download at http://bioinfo.au.tsinghua.edu.cn/pbeam/

Citation

Peng et al. Bioinformation 3(8): 349-351 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.