Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33 2583–2585.

Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106 (3): 411-422

Version info: 

v2.1, 2020-08-25


MISA-web - creates the Primer3 input file - 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 modeling software Primer3 (Whitehead Institute) may work in order to design primers flanking the microsatellite locus. For usage and installation of Primer3 see

Archived obsolete versions of and can be found under this link. Note that these are preserved for compatibility with older versions of Primer3 (older than Release Version 2.5.0).

Syntax: <project name.misa>

<project name.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 FASTA sequence file needs to be accessible as well.

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

Syntax: <project name.p3out> <project name.misa>

This tool parses the Primer3 output file (project name.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 creating a new file (project name.results).