NAME

Bio::Polloc::Typing::bandingPattern::amplification - banding-pattern-based methods for typing assessment using amplification

DESCRIPTION

Category 1 of genotyping methods in:

  Li, W., Raoult, D., & Fournier, P.-E. (2009).
  Bacterial strain typing in the genomic era.
  FEMS Microbiology Reviews, 33(5), 892-916.

IMPLEMENTS OR EXTENDS

• Bio::Polloc::Typing::bandingPattern

AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

APPENDIX

Methods provided by the package

new

Generic initialization method

METHODS FROM Bio::Polloc::TypingI

scan

cluster

typing_value

graph_content

METHODS FROM Bio::Polloc::Typing::bandingPattern

fragments

min_size

max_size

SPECIFIC METHODS

design_primers

Designs the primers to amplify all the loci in the group.

Arguments

-locigroup Bio::Polloc::LociGroup

The loci to be amplified.

Returns

A <Bio::Polloc::Polloc::IO> object pointing to a file containing the primers designed in the format required by EMBOSS primerseq:

  NAME_1  FWD-SEQ  REV-SEQ
  ...

primer_conservation

Gets/sets the minimum conservation of a region to design primers. 1 by default.

primer_size

Gets/sets the primer size. 20 by default.

flanking_size

Gets/sets the size of the flanking region to take into account for the primer design. 500 by default.

annealing_errors

Gets/sets the maximum percentage of errors allowed for a primer to anneal. 0 by default.

INTERNAL METHODS

Methods intended to be used only within the scope of Bio::Polloc::*

_initialize

_initialize_method

cpanm Bio::Polloc

perl -MCPAN -e shell
install Bio::Polloc