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Published online 2 January 2004

Nucleic Acids Research, 2004, Vol. 32, No. 1 e5
© 2004 Oxford University Press

SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development

Thomas Thiel, Raja Kota, Ivo Grosse, Nils Stein and Andreas Graner*

Institute for Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany

*To whom correspondence should be addressed. Tel: +49 39482 5521; Fax: +49 39482 5155; Email: graner{at}ipk-gatersleben.de
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

With the influx of various SNP genotyping assays in recent years, there has been a need for an assay that is robust, yet cost effective, and could be performed using standard gel-based procedures. In this context, CAPS markers have been shown to meet these criteria. However, converting SNPs to CAPS markers can be a difficult process if done manually. In order to address this problem, we describe a computer program, SNP2CAPS, that facilitates the computational conversion of SNP markers into CAPS markers. 413 multiple aligned sequences derived from barley ESTs were analysed for the presence of polymorphisms in 235 distinct restriction sites. 282 (90%) of 314 alignments that contain sequence variation due to SNPs and InDels revealed at least one polymorphic restriction site. After reducing the number of restriction enzymes from 235 to 10, 31% of the polymorphic sites could still be detected. In order to demonstrate the usefulness of this tool for marker development, we experimentally validated some of the results predicted by SNP2CAPS.


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