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.

Programs

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

Data

The data for the database schema nordborg_96 was downloaded from http://walnut.usc.edu/2010, 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!)