Microsatellite finder in 454 data Files

MicrofinderLITE.py simply looks for repeats. Its usage is very simple:
Parameters which must be entered in command line for program to run: inputfile.fna, minimum number of repeats, length of flanking region>outputfile.txt

Example: python MicrofinderLITE.py inputfilename.fna 4 50 > outputfilename.txt

This will give you anything that repeats at least four times and has 50bp of flanking sequence for primer development.

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If you want to be a bit fancier and figure out what your putative microsatellites are try MicroFinder.py:

Microfinder.py associates the best microsat candidates with their best blast hits. Biopython has to be installed to use this version. You also need an xml formatted database of what the top blast hits were for each read. To get this file, you run a local blast on your 454 sequences and retrieved the output as an xml format (it explains how to do this in the blast manual).

Parameters which must be entered in command line for program to run: inputfile.fna, minimum number of repeats, length of flanking region, xmlparsedblast.xml file

Example: python Microfinder.py inputfilename.fna 4 50 xmlinputfilename.xml > outputfilename.txt

This will give you anything that repeats at least four times and has 50bp of flanking sequence for primer development and their best blast hit.