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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·Marilyn I Andersen
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Abstract

UNLABELLED: 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.

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Computer GraphicsDatabase Management SystemsGene Expression ProfilingGenotypeInformation Storage and RetrievalOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideSequence Analysis, DNASystems IntegrationUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

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Scott J Tebbutt, Igor V Opushnyev, Ben W Tripp, Ayaz M Kassamali, Wendy L Alexander, Marilyn I Andersen. 2004-08-12. SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data.. https://doi.org/10.1093/bioinformatics%2Fbth470

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