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Bioinformatics Advance Access originally published online on September 4, 2007
Bioinformatics 2007 23(20):2784-2787; doi:10.1093/bioinformatics/btm428
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MSQT for choosing SNP assays from multiple DNA alignments

Norman Warthmann , Joffrey Fitz and Detlef Weigel *

Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tübingen, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: One challenging aspect of genotyping and association mapping projects is often the identification of markers that are informative between groups of individuals and to convert these into genotyping assays.

Results: The Multiple SNP Query Tool (MSQT) extracts SNP information from multiple sequence alignments, stores it in a database, provides a web interface to query the database and outputs SNP information in a format directly applicable for SNP-assay design. MSQT was applied to Arabidopsis thaliana sequence data to develop SNP genotyping assays that distinguish a recurrent parent (Col-0) from five other strains. SNPs with intermediate allele frequencies were also identified and developed into markers suitable for efficient genetic mapping among random pairs of wild strains.

Availability: The source code for MSQT is available at http://msqt.weigelworld.org, together with an online instance of MSQT containing data on 1214 sequenced fragments from 96 ecotypes (wild inbred strains) of the reference plant A.thaliana. All SNP genotyping assays are available in several formats for broad community use.

Contact: weigel{at}weigelworld.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on June 26, 2007; revised on July 27, 2007; accepted on August 16, 2007

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