Bio::CUA - Codon Usage Analyzer. River stage zero No dependents

The aim of this distribution is to provide comprehensive and flexible tools to analyze codon usage bias (CUB) and relevant problems, so that users can speed up the genetic research by taking advantage of this convenience. One amino acid can be encode...

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::Seq - a module processing sequence object River stage zero No dependents

This module is called by Bio::CUA::SeqIO to create sequence object which has some basic methods required by the modules in the distribution <http://search.cpan.org/dist/Bio-CUA/>. The purpose of this module is to increase the portability of the distr...

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::CUB - This is the parent class for all classs processing codon usage bias (CUB). River stage zero No dependents

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::SeqIO - a package to parse sequence file if module Bio::SeqIO is unavailable in the system. River stage zero No dependents

This is an auxiliary module to process sequences in case the module Bio::SeqIO is not installed in the system. At present, this module can only process fasta-formatted sequence file....

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::Tutorial - A tutorial on using the programs of Bio-CUA River stage zero No dependents

This is a tutorial on how to use the accompanying programs in the distribution. The three programs are: cai_codon.pl tai_codon.pl cub_seq.pl If running any program without giving parameters, it will show a brief usage information. To learn how to wri...

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::CodonTable - A package processing genetic codon table River stage zero No dependents

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::Summarizer - a class to summarize features of sequences. River stage zero No dependents

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::CUB::Builder - A module to calculate codon usage bias (CUB) metrics at codon level and other parameters River stage zero No dependents

Codon usage bias (CUB) can be represented at two levels, codon and sequence. The latter is often computed as the geometric means of the sequence's codons. This module caculates CUB metrics at codon level. Supported CUB metrics include CAI (codon adap...

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

Bio::CUA::CUB::Calculator - A module to calculate codon usage bias (CUB) indice for protein-coding sequences River stage zero No dependents

Codon usage bias (CUB) can be represented at two levels, codon and sequence. The latter is often computed as the geometric means of the sequence's codons. This module caculates CUB metrics at sequence level. Supported CUB metrics include CAI (codon a...

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

cub_seq.pl - a program to calculate sequence codon usage bias metrics and other sequence parameters. River stage zero No dependents

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

tai_codon.pl - a program to calculate tAI of each codon River stage zero No dependents

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

cai_codon.pl - a program to calculate CAI for each codon River stage zero No dependents

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

tabulate_codons.pl - a program to output codons in a sequence file as a table River stage zero No dependents

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC

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