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

Jong Hyun Kim; Woo Cheol Kim; Michael S. Waterman; Sanghyun Park; Lei M. Li

doi:10.1093/bioinformatics/btp399

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

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

College of Computing

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	2430-2431
Number of pages	2
Journal	Bioinformatics
Volume	25
Issue number	18
DOIs	https://doi.org/10.1093/bioinformatics/btp399
Publication status	Published - 2009 Sept

Bibliographical note

Funding Information:
Funding: The Korea Science and Engineering Foundation, Ministry of Sciences & Technology (2007-03965 to J.H.K., W.K. and S.P.); The National Institutes of Health, USA (HG002790 to M. S. W. and L. M. L.).

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btp399

Cite this

@article{365c234522ca44b1a740765e099a1d5d,

title = "HAPLOWSER: A whole-genome haplotype browser for personal genome and metagenome",

abstract = "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.",

author = "Kim, {Jong Hyun} and Kim, {Woo Cheol} and Waterman, {Michael S.} and Sanghyun Park and Li, {Lei M.}",

note = "Funding Information: Funding: The Korea Science and Engineering Foundation, Ministry of Sciences & Technology (2007-03965 to J.H.K., W.K. and S.P.); The National Institutes of Health, USA (HG002790 to M. S. W. and L. M. L.).",

year = "2009",

month = sep,

doi = "10.1093/bioinformatics/btp399",

language = "English",

volume = "25",

pages = "2430--2431",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "18",

}

TY - JOUR

T1 - HAPLOWSER

T2 - A whole-genome haplotype browser for personal genome and metagenome

AU - Kim, Jong Hyun

AU - Kim, Woo Cheol

AU - Waterman, Michael S.

AU - Park, Sanghyun

AU - Li, Lei M.

N1 - Funding Information: Funding: The Korea Science and Engineering Foundation, Ministry of Sciences & Technology (2007-03965 to J.H.K., W.K. and S.P.); The National Institutes of Health, USA (HG002790 to M. S. W. and L. M. L.).

PY - 2009/9

Y1 - 2009/9

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=69849114202&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=69849114202&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btp399

DO - 10.1093/bioinformatics/btp399

M3 - Article

C2 - 19561337

AN - SCOPUS:69849114202

SN - 1367-4803

VL - 25

SP - 2430

EP - 2431

JO - Bioinformatics

JF - Bioinformatics

IS - 18

ER -

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

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this