Journal Article

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

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

in Bioinformatics

Volume 25, issue 18, pages 2430-2431
Published in print September 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp399
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome

More Like This

Show all results sharing this subject:

  • Bioinformatics and Computational Biology

GO

Show Summary Details

Preview

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 functional annotations and custom tracks. The associations are quantified 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@cs.yonsei.ac.kr; lilei@usc.edu

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

Journal Article.  1200 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.