Skip Navigation


Bioinformatics Advance Access originally published online on January 25, 2009
Bioinformatics 2009 25(5):662-663; doi:10.1093/bioinformatics/btp017
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
25/5/662    most recent
btp017v2
btp017v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Martin, O.
Right arrow Articles by Stevenson, B. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Martin, O.
Right arrow Articles by Stevenson, B. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context

Olivier Martin 1,{dagger}, Armand Valsesia 1,2,{dagger}, Amalio Telenti 3, Ioannis Xenarios 1 and Brian J. Stevenson 1,2,*

1Swiss Institute of Bioinformatics, 2Ludwig Institute for Cancer Research, 1015 Lausanne and 3Institute of Microbiology, University Hospital, University of Lausanne, 1011 Lausanne, Switzerland

*To whom correspondence should be addressed.


  Abstract

Summary: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets.

Availability: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

Contact: brian.stevenson{at}licr.org

Supplementary information: Supplementary data are available at http://sourceforge.net/projects/associationview/ online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: John Quackenbush

Received on September 16, 2008; revised on December 16, 2008; accepted on January 5, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Circ Cardiovasc GenetHome page
A. D. Johnson
Single-Nucleotide Polymorphism Bioinformatics: A Comprehensive Review of Resources
Circ Cardiovasc Genet, October 1, 2009; 2(5): 530 - 536.
[Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.