MISA - MIcroSAtellite identification tool

Download misa.ini - example of a specification file

Syntax: misa.pl <FASTAfile>

Declarations:

<FASTAfile> is the filename containing DNA sequences in FASTA format.
An additional file containing the search parameters is required named "misa.ini".

In a single line beginning with "def" a sequence of number pairs is expected, whereas the first number defines the unit sizes and the second number the lower threshold of repeats for that specific unit.
In a single line beginning with "int" a single number is expected defining the maximal number of bases between two adjacent microsatellites to be recognised as being a compound microsatellite.

Output:

Results of the microsatellite search are stored in two files:

In "<FASTfile>.misa" the localization and type of identified microsatellite(s) are stored in a tablewise manner.
The file "<FASTfile>.statistics" summarizes different statistics as the frequency of a specific microsatellite type according to the unit size or individual motifs.

UPDATE:

27/09/2010: Small bug fix for the SSR frequency table in which motif groups are summarized