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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Authors: Stephan Ossowski; Korbinian Schneeberger; Richard M Clark; Christa Lanz; Norman Warthmann; Detlef Weigel Journal: Genome Res Date: 2008-09-25 Impact factor: 9.043
Authors: Silvia Busoms; Joana Teres; Xin-Yuan Huang; Kirsten Bomblies; John Danku; Alex Douglas; Detlef Weigel; Charlotte Poschenrieder; David E Salt Journal: Plant Physiol Date: 2015-06-01 Impact factor: 8.340
Authors: Alexander Platt; Matthew Horton; Yu S Huang; Yan Li; Alison E Anastasio; Ni Wayan Mulyati; Jon Agren; Oliver Bossdorf; Diane Byers; Kathleen Donohue; Megan Dunning; Eric B Holub; Andrew Hudson; Valérie Le Corre; Olivier Loudet; Fabrice Roux; Norman Warthmann; Detlef Weigel; Luz Rivero; Randy Scholl; Magnus Nordborg; Joy Bergelson; Justin O Borevitz Journal: PLoS Genet Date: 2010-02-12 Impact factor: 5.917
Authors: Stephanie Plantegenet; Johann Weber; Darlene R Goldstein; Georg Zeller; Cindy Nussbaumer; Jérôme Thomas; Detlef Weigel; Keith Harshman; Christian S Hardtke Journal: Mol Syst Biol Date: 2009-02-17 Impact factor: 11.429
Authors: Helen I Field; Serena A Scollen; Craig Luccarini; Caroline Baynes; Jonathan Morrison; Alison M Dunning; Douglas F Easton; Paul D P Pharoah Journal: BMC Bioinformatics Date: 2009-06-12 Impact factor: 3.169