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Welcome to MSQT!

MSQT is a SNP Query Tool.

It was developed to make polymorphism information readily accessible and to assist researchers in selecting distinct sequence changes and developing SNP detection assays. learn more >>

The software is open source and available under the terms of the GNU General Public License (GPL). download >>


Version 0.7.3 released for download.
There was a bug in SNIPE4SNPS version 0.7.2. If you are using MSQT/SNIPED! it is highly recommended to update your installation.
The online installation for the Nordborg data was not affected.

MSQT for choosing SNP assays from multiple DNA alignments was evaluated by
Faculty of 1000 Biology: evaluations for Warthmann N et al Bioinformatics 2007 Sep 4 : http://www.f1000biology.com/article/id/1091281/evaluation

Our paper on MSQT has appeared in Bioinformatics.
If you find the tool (and/or the data it provides) useful for your work, then please cite:
Norman Warthmann, Joffrey Fitz and Detlef Weigel.
MSQT for choosing SNP assays from multiple DNA alignments.
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm428

Version 0.7.2 released for download.
Fixed a layout issue relating to IE.
A demo version with some hypothetical datasets (my_dogs, my_cats, etc) is online now. Feel free to test MSQT/Admin for this installation.

We released version 0.7.1 We fixed some layout bugs and updated the online documentation for MSQT/Admin. Today we also released this project web site.

We released version 0.7. This minor update includes
  • New layout
  • Password protection for MSQT/Admin
We released version 0.6. Major features are:
  • Added installation scripts
  • New layout for MSQT/Sniped!
  • Better dataset population and management tool (MSQT/Admin)
  • New example data in source distribution
  • Support for alleles in IUB-Code
  • Introduced internal module communication with XML
  • Experimental support for SOAP/WSDL Webservices
  • SNP parser rewritten (it's faster and we do not need BioPerl anymore)
  • msqt has moved to a new home and can be reached now at http://msqt.weigelworld.org. http://eb.tuebingen.mpg.de/msqt/ is deprecated but will be available for a few more days.
  • On April 20th, 2006, Magnus Nordborg released new and updated data (http://walnut.usc.edu/apache2-default/2010/). We loaded this data into a new schema, "nordborg_96". This is the default from now on. The schema "nordborg_99" is deprecated.
I have updated the documentation; should be good for two weeks or so ;)

Release of Version 0.5 for public access.
There are new features and minor bugfixes:
  • Due to mystic ons and offs of the jalview alignement viewer, we decided to replace it by a different viewer written and donated by Joffrey: "Alivie". Look and feel should be the same/better ;-)
  • Upon poweruser request we've developed a completely new concept to query the SNP database: with MSQT/SNIPED! you are querying a database table filled with SNPs and corresponding ADF output, pre-selected for allele frequencies and such. Please consult the documentation for further information.
Release of Version 0.4 for public access.
There are new features (integration of assay information, optional annotation of additional ecotypes) and some minor bugfixes. Please consult the documentation for further information.

Version 0.2 of MSQT is now ready and internally released. Changes are: A database redesign, some layout improvements and a partial code refactoring.
Because of the database redesign there are minor changes of the GUI. Especially MSQT-E users should consult the documentation due to altered table structurs.

Today I fixed all incomplete alignments and reloaded the databases; now all should be fine. However, it is always a good idea to view the alignments. ;-)

We noticed today that some of the original alignments are incomplete. There are ecotypes missing. This of course overestimates the number of SNPs, because there is missing data which we don't know about. We are fixing this right now. Until further notice the safest thing to do is to verify the SNPs chosen with the alignments.

Today we made MSQT public at http://www.eb.tuebingen.mpg.de/msqt/.

Today we released the first stable version of MSQT.


MSQT was published by Bioinformatics.

Fulltext >>

Abstract on PubMed >>

Nordborg data

Dataset from 96 ecotypes of Arabidopsis thaliana

Click here to start MSQT >>


View Screenshots of the Web Application here >>

Online Demo

Try our demo version to test MSQT. Start here >>

Latest releases

MSQT Web Application 0.7.3

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