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Nucleic Acids Research 2006 34(Web Server issue):W477-W481; doi:10.1093/nar/gkl215
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

CAPweb: a bioinformatics CGH array Analysis Platform

Stéphane Liva1,*, Philippe Hupé1,2, Pierre Neuvial1, Isabel Brito1, Eric Viara1, Philippe La Rosa1 and Emmanuel Barillot1

1 Institut Curie, Service Bioinformatique 26 rue d'Ulm, 75248 Paris Cedex 05, France 2 Institut Curie CNRS UMR 144, 26 rue d'Ulm, 75248 Paris Cedex 05, France

*To whom correspondence should be addressed. Tel: +33 0 1 4234 65 31; Fax: +33 0 1 42 34 65 28; Email: capweb{at}curie.fr

Received February 14, 2006. Revised March 24, 2006. Accepted March 24, 2006.

Assessing variations in DNA copy number is crucial for understanding constitutional or somatic diseases, particularly cancers. The recently developed array-CGH (comparative genomic hybridization) technology allows this to be investigated at the genomic level. We report the availability of a web tool for analysing array-CGH data. CAPweb (CGH array Analysis Platform on the Web) is intended as a user-friendly tool enabling biologists to completely analyse CGH arrays from the raw data to the visualization and biological interpretation. The user typically performs the following bioinformatics steps of a CGH array project within CAPweb: the secure upload of the results of CGH array image analysis and of the array annotation (genomic position of the probes); first level analysis of each array, including automatic normalization of the data (for correcting experimental biases), breakpoint detection and status assignment (gain, loss or normal); validation or deletion of the analysis based on a summary report and quality criteria; visualization and biological analysis of the genomic profiles and results through a user-friendly interface. CAPweb is accessible at http://bioinfo.curie.fr/CAPweb.


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