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Bioinformatics Advance Access originally published online on March 24, 2007
Bioinformatics 2007 23(12):1550-1552; doi:10.1093/bioinformatics/btm122
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SNPTools: a software tool for visualization and analysis of microarray data

Frank J. Sørensen 1, Claus L. Andersen 2 and Carsten Wiuf 1,2,*

1Bioinformatics Research Center, University of Aarhus, Høegh Guldbergs Gade 10, Building 1090, DK-8000 Aarhus C and 2Molecular Diagnostic Laboratory, Aarhus University Hospital, Brendstrupgaardsvej 100, DK-8200 Aarhus N, Denmark

*To whom correspondence should be addressed.


  Abstract

Summary: 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.

Availability: The software, example data sets and tutorials are freely available from http://www.birc.au.dk/snptools

Contact: wiuf{at}birc.au.dk

Associate Editor: Chris Stoeckert

Received on January 11, 2007; revised on February 28, 2007; accepted on March 20, 2007

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