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Bioinformatics Advance Access originally published online on August 12, 2004
Bioinformatics 2005 21(1):124-127; doi:10.1093/bioinformatics/bth470
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Bioinformatics vol. 21 issue 1 © Oxford University Press 2005; all rights reserved.

SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data

Scott J. Tebbutt *, Igor V. Opushnyev , Ben W. Tripp , Ayaz M. Kassamali , Wendy L. Alexander and Marilyn I. Andersen

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6

*To whom correspondence should be addressed.

Summary: SNP Chart is a Java application for the visualization and interpretation of microarray genotyping data primarily derived from arrayed primer extension-based chemistries. Spot intensity output files from microarray analysis tools are imported into SNP Chart, together with a multi-channel TIFF image of the original array experiment and a list of the actual single nucleotide polymorphisms (SNPs) being tested. Data from different and/or replicate probes that interrogate the same SNP, but that are scattered across the array grid, can be reassembled into a single chart format, specific for the SNP. This allows a quick and very effective ‘visualization’/‘quality control’ of the data from multiple probes for the same SNP that can be easily interpreted and manually scored as a genotype.

Availability: http://www.snpchart.ca

Contact: stebbutt{at}mrl.ubc.ca

Supplementary information: A comprehensive manual describing SNP Chart is available at the above website, together with sample data files.

Received on May 27, 2004; revised on July 13, 2004; accepted on August 8, 2004

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