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MSQT - Multiple SNP Query Tool

Welcome to MSQT!

MSQT is a SNP Query Tool. It was developed to make available polymorphism information readily accessible and to assist researchers in selecting distinct sequence changes and developing SNP detection assays.


We provide several tools for SNP mining and analysis.

  • MSQT/SBE: SNPs Between Ecotypes; finds distinct SNPs between two sets of ecotypes
  • MSQT/ADF: Assay Development Formatter; annotates polymorphisms
  • MSQT/E: Expert mode; direct interface to the databases
  • MSQT/SNIPED!: query interface to a precompiled SNP database; works via the expert mode

How to cite:

Norman Warthmann, Joffrey Fitz and Detlef Weigel.
MSQT for choosing SNP assays from multiple DNA alignments.
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm428


The data for the database schema nordborg_96 was downloaded from, on May, 3rd 2006. Most of this data is published:

Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J.
The pattern of polymorphism in Arabidopsis thaliana
PLoS Biology 2005 Jul;3(7):e196. Epub 2005 May 24 (open access!)