fasta_regex.pl - Find sequence motifs in a (multi) Fasta file
fasta_regex.pl [--motif REGEX] [--fa FILE] [--name STRING] [--bed] [options]
This script extracts sequence motifs, provided as regular expressionm from Fasta files.
The tool returns all motifs matching the search criteria as a (mutli-)Fasta file to STDOUT. This means if the motif is found more than once within an annotated feature, all matches will be reported. Optionally, all loci matching the regular expresion pattern are reorted as BED6 intervals.
Reference genome in Fasta format
The motif to search for as regular expression.
Switch for printing BED6 intervals of matching motif loci.
Optional name for BED6 intervals.
Michael T. Wolfinger <email@example.com>
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell
For more information on module installation, please visit the detailed CPAN module installation guide.