FindMotif

From Mswiki

This script will find all the sequences in a FASTA file containing a motif indicated by the user. The motif is represented by a regular expression tag.

An example:

/data/6/jrjohns1/perlscripts/FindMotif database.fasta "GAATTC"

Would search database.fasta for the motif GAATTC.

GAATT[CG] would search for GAATTC or GAATTG.

GA?TTC would allow any character where the ? is place.

See here for more complex regular expression patterns.