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


BACKGROUND
http://www.snpchart.ca.
Tebbutt
Scott J
SJ
James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada. stebbutt@mrl.ubc.ca
Opushnyev
Igor V
IV
Tripp
Ben W
BW
Kassamali
Ayaz M
AM
Alexander
Wendy L
WL
Andersen
Marilyn I
MI
D003196:Computer Graphics; D003628:Database Management Systems; D020869:Gene Expression Profiling / Q000379:methods*; D005838:Genotype; D016247:Information Storage and Retrieval / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D018511:Systems Integration; D014584:User-Computer Interface