title: MSQT for choosing SNP assays from multiple DNA alignments.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tübingen, Germany.
authors.forename: Norman
authors.initials: N
authors.lastname: Warthmann
authors.forename: Joffrey
authors.initials: J
authors.lastname: Fitz
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D005819:Genetic Markers / Q000235:genetics; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface