Primer3 interface modules

Download p3_in.pl - creates the Primer3 input file
Download p3_out.pl - parses the Primer3 output file

These perl scripts are an example of how an interaction with the results obtained by the microsatellite search using the MISA tool and the primer modelling software Primer3 (Whitehead Institute) may work in order to design primers flanking the microsatellite locus. For usage and installation of Primer3 see http://www-genome.wi.mit.edu/genome_software/other/primer3.html.
 


Syntax: p3_in.pl <FASTAfile.misa>

<FASTAfile.misa> is one of the files which was created by MISA containing information about the type and the localization of each individual microsatellite. Since the DNA sequence is also submitted to Primer3, the original <FASTAfile> needs to be accessible as well.

The created file <FASTAfile.p3in> is the input file for Primer3, which can then be invoked as "primer3_core <FASTAfile.p3in >FASTAfile.p3out".
 

Syntax: p3_out.pl <FASTAfile.p3out> <FASTAfile.misa>

This tool parses the Primer3 output file (FASTAfile.p3out) for the calculated primer sequences, their position and melting temperatures as well as the expected PCR product size and merges this information together with the data from the file <FASTAfile.misa> creating a new file (FASTAfile.results).