News

3/29/09: If you plan to checkout code from SVN, I am in the process of rewriting the guts of the microsatellite-locating code. All of the changes are ONLY present in the commandline directory of SVN. Expect several of the listed commandline options to be a bit flaky for the next day or 2, although the code is working and testing OK.

3/29/08: The manuscript is available free from Blackwell: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2007.01884.x

12/12/07: The manuscript has been released for printing (i,e. citation information updated)

8/22/07: The FAQ has been updated with more information on tags and tagging.

If you have constructive feedback (likes, dislikes, enhancements), please send an email to the list-serve. All suggestions are welcomed and will be considered.

Purpose

msatcommander is a python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatfinder 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).

msatcommander will also design and tag primers using primer3 as its primer design engine (see References for citations). Many thanks to the primer3 team, in general, and Steve Rozen, in particular. Additional information regarding primer3 may also be found on the primer3 wiki.

Citation

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.

I would be more than happy to provide you with a pdf of the above, if needed.

Supported OSs

NOTE: msatcommander will not work on OS X < 10.4.x

Differences from other programs

• searches for all mono-,di-,tri-,tetra-,penta-, and hexanucleotide repeats
• repeats may be combined across user-specified distances (bp)
• designs primers for located repeats
• tags and tests primers with m13R, CAG, or custom tag. The 'best' primer is reported to the user
• offers a convenient GUI for a majority of users
• outputs results in csv format, for easy importation to spreadsheet software

Input

msatcommander will read FASTA-formatted files of single or multiple sequences. These files may end in '.fsa', '.fasta', or '.txt'.

Output

For array searching, the user may select and name a specific output file. When searching, designing, and/or tagging primers, the user must select or create and select a directory to contain the output. In this case, the output consists of the following:

• microsatSearchOutput.csv (contains microsatellite search results)
• primerCombined.csv (optional; contains combined microsatellite search results)
• a primer3 directory
• formatted text files for each designed primer
• primerNoTag.csv (contains untagged primer sequences)
• primerTag.csv (optional; contains tagged primers)

Reporting Bugs

Please report bugs via the issues tab. If you have a question about something that may be a bug, please send an email to the list-serve.

About

msatcommander is written in python and makes use of the biopython and wxPython modules. msatcommander uses primer3 as its primer design engine. Primer3 source is C and Perl. Primer3 was written by Steve Rozen and Helen Skaletsky. primer3_core binaries (provided within the msatcommander binaries) are built specifically for each architecture (OSX or WindowsXP). The primer3 OSX binary is universal.