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

Scott J. Tebbutt | Zendy; Igor V. Opushnyev | Zendy; Ben Tripp | Zendy; Ayaz M. Kassamali | Zendy; Wendy L. Alexander | Zendy; Marilyn I. Andersen | Zendy

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

Author(s) -

Scott J. Tebbutt,

Igor V. Opushnyev,

Ben Tripp,

Ayaz M. Kassamali,

Wendy L. Alexander,

Marilyn I. Andersen

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth470

Subject(s) - snp , computer science , replicate , visualization , chart , genotyping , snp genotyping , data mining , snp array , single nucleotide polymorphism , data visualization , computational biology , biology , genotype , genetics , statistics , mathematics , gene

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.

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