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Nucleic Acids Research 2007 35(Database issue):D71-D75; doi:10.1093/nar/gkl806
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Nucleic Acids Research, 2007, Vol. 35, Database issue D71-D75
© 2006 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.

Articles

SNPSTR: a database of compound microsatellite-SNP markers

I. Agrafioti1,* and M. P. H. Stumpf1,2,*

1 Centre for Bioinformatics, Division of Molecular Biosciences London, UK 2 Institute of Mathematical Sciences, Imperial College London London, UK

*To whom correspondence should be addressed at Centre for Bioinformatics, Wolfson Building, London SW7 2AZ, UK. Tel: +44 20 7594 5114; Fax: +44 20 7594 5789; Email: m.stumpf{at}imperial.ac.uk

Received August 9, 2006. Revised September 27, 2006. Accepted September 29, 2006.

There has been widespread and growing interest in genetic markers suitable for drawing population genetic inferences about past demographic events and to detect the effects of selection. In addition to single nucleotide polymorphisms (SNPs), microsatellites (or short tandem repeats, STRs) have received great attention in the analysis of human population history. In the SNPSTR database (http://www.imperial.ac.uk/theoreticalgenomics/data-software) we catalogue a relatively new type of compound genetic marker called SNPSTR which combines a microsatellite marker (STR) with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 bp apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers. Thus, SNPSTRs have the potential to become a very useful tool in the field of population genetics. The SNPSTR database contains all inferable human SNPSTRs as well as those in mouse, rat, dog and chicken, i.e. all model organisms for which extensive SNP datasets are available.

*Correspondence may also be addressed to I. Agrafioti. Tel: +44 20 7594 5114; Fax: +44 20 7594 5789; Email: ino.agrafioti{at}imperial.ac.uk


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