AUTHOR

Luis M. Rodriguez-R < lmrodriguezr at gmail dot com >

DESCRIPTION

polloc_primers.pl - Designs primers to amplify the groups of loci in the given genomes and attempts to run an in silico PCR.

LICENSE

This script is distributed under the terms of The Artistic License. See LICENSE.txt for details.

SYNOPSIS

perl polloc_vntrs.pl arguments

The arguments must be in the following order:

Input gff

GFF3 file containing the loci to amplify.

Example: "/tmp/polloc-vntrs.out.gff".

Groups

File containing the IDs of the grouped loci. One line per group, and the IDs separated by spaces.

Example: "/tmp/polloc-vntrs.out.groups".

Output

Path to the base of the output files.

Example: "/tmp/polloc-primers.out".

Draw

Should I produce graphical output? Any non-empty string to generate PNG images, or empty string ('') to ignore graphical output.

Consensus (float)

Consensus percentage for primers design.

Default: 100.

Length (int)

Length of the primers.

Default: 20.

Errors (int)

Percentage of allowed mismatches during *in silico* amplification.

Default: 0.

Names

The names of the genomes separated by colons (:). Alternatively, it can be an empty string ('') to assign genome names from files.

Example: "Xci3:Xeu8:XamC"

Inseqs

Sequences to scan (input). Each argument will be considered a single genome, and the values of 'names' will be applied. The order of the inseqs must be the same of the names.

Example 1: "/data/Xci3.fa" "/data/Xeu8.fa" "/data/XamC.fa"

Example 2: /data/X*.fa (unquoted)

Run perl polloc_primers.pl without arguments to see the help message.

SEE ALSO

• Bio::Polloc::LocusIO

• Bio::Polloc::Genome

• Bio::Polloc::TypingI