Microarrays Research Today is a free monthly online journal that collates and summarizes the latest research about Microarrays, including details on experiments, designs, statistics, analysis, software.

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

Tebbutt SJ, Opushnyev IV, Tripp BW, Kassamali AM, Alexander WL, Andersen MI

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada. stebbutt@mrl.ubc.ca

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.

Published 4 January 2005 in Bioinformatics, 21(1): 124-7.
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