NAME

motiffinda.pl - Find sequence motifs in annotated features.

SYNOPSIS

motiffinda.pl [--motif REGEX] [--gff FILE] [--fa FILE] [options]

DESCRIPTION

This script extracts sequence motifs from gene annotation data. The motif can be provided as regualr expression. Optionally, only motifs in frame with the annoation are reported.

The tool returns all motifs matching the search criteria as a (mutli-)Fasta file to STDOUT. This means if teh motif is found more than once within an annotated feature, all matches will be reported.

OPTIONS

motif|m

The motif to search for as regular expression. For technical reasons, the regular expression must be enclosed in brackets ().

gff|g

Genome annotation in GFF3 format

fa|f

Reference genome in Fasta format

gbkey

Motifs are only searched for in this feature type, aka Genbank key (e.g. CDS or gene). Currently only one Genbank key provided via this option will be procesed.

offset|o

Offset for determination of frame

<inframe|i>

Only report motifs in current ORF

AUTHOR

Michael T. Wolfinger <michael@wolfinger.eu>