Bio::Palantir::Explorer - front-end class for Bio::Palantir::Explorer module, wich handles the NRPS/PKS domain exploration without pre-existing consensus architecture
version 0.211420
This module implements classes and their methods for exploring NRPS/PKS domain architecture without any previous consensus imposed. Note that this application mode is only based on the expertise of the user. The input used by Palantir::Refiner is the FASTA file of a NRPS/PKS BGC (e.g., nrps_bgc.fasta), which can be extracted from antiSMASH HTML webpages or with the script bin/extract_fasta.pl (which uses Palantir::Parser).
Palantir::Refiner
bin/extract_fasta.pl
Palantir::Parser
The exploratory Biosynthetic Gene Cluster (BGC) information is hierarchically organized as follows:
ClusterFasta.pm: contains attributes and methods for the BGC Cluster level, including an array of GeneFasta objects
ClusterFasta.pm
GeneFasta.pm: contains attributes and methods for the BGC Gene level, including an array of DomainPlus objects (if NRPS/PKS BGCs)
GeneFasta.pm
DomainPlus.pm: contains attributes and methods for the BGC Domain level
DomainPlus.pm
The Domain information is inherited from Palantir::Refiner::DomainPlus, and as no consensus architecture is defined, Module information is not applicable.
Palantir::Refiner::DomainPlus
Loic MEUNIER <lmeunier@uliege.be>
This software is copyright (c) 2019 by University of Liege / Unit of Eukaryotic Phylogenomics / Loic MEUNIER and Denis BAURAIN.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install Bio::Palantir, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Palantir
CPAN shell
perl -MCPAN -e shell install Bio::Palantir
For more information on module installation, please visit the detailed CPAN module installation guide.