News

06/25/2011: Added ability to input *.fna files. Fixed an error with microsat scanning that caused program to hang. 1.0.8 available in Downloads

This is prerelease software - and you should use it carefully. Please report any bugs to the mailing list or directly to me. The binary version of msatcommander (available for download) is for OSX 10.6 and greater only. If you are using 10.5 or earlier, you will need to checkout the source code instead.

Now, here's what it looks like:

Feedback

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. 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).

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

Since primer3 is an integral part of msatcommander, please cite both of the following manuscripts:

• 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.

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

Supported OSs (msatcommander >= 1.0.0)

NOTE 1: msatcommander 1.0.0 or greater will not work on OS X < 10.6 NOTE 2: I am working on compiling a Windows binary for XP and potentially Windows 7

Supported OSs (msatcommander < 0.8.x)

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
• adds GTTT pigtails to the un-tagged, 'best' primer 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.