SNPTools: a software tool for visualization and analysis of microarray data.
CONCLUSIONS
We have created a software tool, SNPTools, for analysis and visualization of microarray data, mainly SNP array data. The software can analyse and find differences in intensity levels between groups of arrays and identify segments of SNPs (genes, clones), where the intensity levels differ significantly between the groups. In addition, SNPTools can show jointly loss-of-heterozygosity (LOH) data (derived from genotypes) and intensity data for paired samples of tumour and normal arrays. The output graphs can be manipulated in various ways to modify and adjust the layout. A wizard allows options and parameters to be changed easily and graphs replotted. All output can be saved in various formats, and also re-opened in SNPTools for further analysis. For explorative use, SNPTools allows various genome information to be loaded onto the graphs.


BACKGROUND
The software, example data sets and tutorials are freely available from http://www.birc.au.dk/snptools
Sørensen
Frank J
FJ
Bioinformatics Research Center, University of Aarhus, Høegh Guldbergs Gade 10, Aarhus C, Denmark.
Andersen
Claus L
CL
Wiuf
Carsten
C
D002874:Chromosome Mapping; D002877:Chromosomes, Human; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D018628:Gene Dosage; D006801:Humans; D019656:Loss of Heterozygosity; D009369:Neoplasms / Q000145:classification / Q000235:genetics / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
D012333:RNA, Messenger