msatcommander is a python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatcommander will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations of repeat types).
application bundles: http://code.google.com/p/msatcommander/downloads/list
documentation: http://brantfaircloth.github.com/msatcommander/ (in progress)
msatcommander will also design and tag primers using primer3 as its primer design engine. Many thanks to the primer3 team, in general, and Steve Rozen, in particular.
When using msatcommander, please cite both of the following publications:
- Faircloth, BC. 2008. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8:92-94. doi:10.1111/j.1471-8286.2007.01884.x
- Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds Krawetz S, Misener S). Humana Press, Totowa, NJ.