Motif Counter

This software counts motifs occurrences in Fasta sequences (DNA, RNA, Protein). Motif Counter is compatible with Perl regular expressions, so any kind of motif can be search of an unlimited list of motifs.

Manual :

1- install Perl free programming language and GNU parallel.

2- unzip the software

3- copy your Fasta files in the “data” directory. For each fasta file a result table is computed.

4- copy the lists of motifs in a text file in the "list" directory

Perl regular expressions are allowed in motifs.

example :

caggagcc

tccacagccc

gaccac{3,}

5- execute the software by the command : perl Motif_count_7.0.pl

6- result tables are in the “results” directory.