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
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
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::*