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Bioinformatics Advance Access published online on August 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth470
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 5, 2004
Revised July 13, 2004
Accepted August 6, 2004

Article

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

Scott J. Tebbutt 1*, Igor V. Opushnyev 1, Ben W. Tripp 1, Ayaz M. Kassamali 1, Wendy L. Alexander 1, Marilyn I. Andersen 1

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

* To whom correspondence should be addressed. E-mail: stebbutt{at}mrl.ubc.ca.


  Abstract

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.

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


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D. C. Walley, B. W. Tripp, Y. C. Song, K. R. Walley, and S. J. Tebbutt
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[Abstract] [Full Text] [PDF]


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