Msatcommander software

Hi all,

This program looks useful, especially for those of you interested in obtaining microsatellites from 454 data or large datasets (e.g. ESTs from Genbank).
It searches fasta files for microsats, and then uses Primer3 for designing primers. We can already do this using Sputnik and Primer3,  but Msatcommander does it all in one program, without the need for editing the format of input/output files.

It looks like the source code and executables for most platforms are available.
Wiki for it here:


One Response to Msatcommander software

  1. Unfortunately the contig assembler program doesnt include gaps or place “n”s for all the non-consensus bases – it annoyingly selects the most common base for the consensus – this is a pain and means every primer set has to be checked by looking at each contig asembly and means we cant use batch design programs (especially for mammals which seem to have more flanking mismatches). Also, I would think that because the majority of the seqs dont have a reverse flank and these repeat programs dont recoginse this often that this would also cause problems. I think we need a better assembly program – if anyone knows of one? and a script that throws out any contigs that dont have a reverse flank.


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