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Bioinformatics Advance Access published online on June 27, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp399
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome

Jong Hyun Kim 1, Woo-Cheol Kim 2, Michael S. Waterman 3, Sanghyun Park 2,* and Lei M. Li 3,*

1Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
2Department of Computer Science, Yonsei University, 134 Shinchon-dong, Seoul, 120-749, Republic of Korea.
3Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1050 Childs way, Los Angeles, CA 90089, USA.

*To whom correspondence should be addressed. Sanghyun Park, E-mail: sanghyun{at}cs.yonsei.ac.kr; Lei M. Li, E-mail: lilei{at}usc.edu


  Abstract

Summary: Haplotype assembly is becoming a very important tool in genome sequencing of human and other organisms. Although haplotypes were previously inferred from genome assemblies, there has never been a comparative haplotype browser that depicts a global picture of whole-genome alignments among haplotypes of different organisms. We introduce a whole-genome HAPLotype brOWSER (HAPLOWSER), providing evolutionary perspectives from multiple aligned haplotypes and functional annotations. Haplowser enables the comparison of haplotypes from metagenomes, and associates conserved regions or the bases at the conserved regions with func-tional annotations and custom tracks. The associations are quanti-fied for further analysis and presented as pie charts. Functional annotations and custom tracks that are projected onto haplotypes are saved as multiple files in FASTA format. Haplowser provides a user-friendly interface, and can display alignments of haplotypes with functional annotations at any resolution.

Availability: Haplowser, written in Java, supports multiple platforms including Windows and Linux. Haplowser is publicly available at http://embio.yonsei.ac.kr/haplowser

Contact: sanghyun{at}cs.yonsei.ac.kr; lilei{at}usc.edu

Supplemental information: Supplemental data are available at http://embio.yonsei.ac.kr/haplowser

Associate Editor: Prof. Dmitrij Frishman

Received on January 26, 2009; revised on June 9, 2009; accepted on June 25, 2009

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