MISA - MIcroSAtellite identification tool
misa.ini - example of a specification file
Syntax: misa.pl <FASTAfile>
<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
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.
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.
27/09/2010: Small bug fix for the SSR frequency table in which motif groups are summarized