codonw(1)

Correspondence Analysis of Codon Usage

Section 1 codonw bookworm source

Description

CODONW

NAME

codonw - Correspondence Analysis of Codon Usage

SYNOPSIS

codonw [inputfile] [outputfile] [bulkoutfile] [options]

DESCRIPTION

CodonW is a package for codon usage analysis. It was designed to simplify Multivariate Analysis (MVA) of codon usage. The MVA method employed in CodonW is correspondence analysis (COA) (the most popular MVA method for codon usage analysis). CodonW can generate a COA for codon usage, relative synonymous codon usage or amino acid usage. Additional analyses of codon usage include investigation of optimal codons, codon and dinucleotide bias, and/or base composition.

OPTIONS

-h

Show help message

-nomenu

Prevent the menu interface being displayed

-nowarn

Prevent warnings about sequences being displayed

-silent

Overwrite files silently

-totals

Concatenate all genes in inputfile

-machine

Machine readable output

-human

Human readable output

-code N

Genetic code as defined under menu 3 option 5

-f_type N

Fop/CBI codons as defined by menu 3 option 6

-c_type N

Cai fitness values as defined by menu 3 option 7

-t (char)

Column separator to be used in output files (comma,tab,space)

Codon usage indices and Amino acid indices

	-cai		calculate Codon Adaptation Index (CAI)
	-fop		calculate Frequency of OPtimal codons index (FOP)
	-cbi		calculate Codon Bias Index (CBI)
	-enc		Effective Number of Codons (ENc)
	-gc		G+C content of gene (all 3 codon positions)
	-gcs3		GC of synonymous codons 3rd positions

-sil_base

Base composition at synonymous third codon positions

-L_sym

Number of synonymous codons

-L_aa

Total number of synonymous and non-synonymous codons

-all_indices

All the above indices

	-aro		Calculate aromaticity of protein
	-hyd		Calculate hydropathicity of protein

-cai_file

{file} User input file of CAI values

-cbi_file

{file} User input file of CBI values

-fop_file

{file} User input file of Fop values

Correspondence analysis (COA) options
-coa_cu

COA of codon usage frequencies

-coa_rscu

COA of Relative Synonymous Codon Usage

-coa_aa

COA of amino acid usage frequencies

-coa_expert

Generate detailed(expert) statistics on COA

-coa_axes N

Select number of axis to record

-coa_num N

Select number of genes to use to identify optimal codons values can be whole numbers or a percentage (5 or 10%)

Bulk output options | only one can be selected per analysis

	-aau		Amino Acid Usage (AAU)
	-raau		Relative Amino Acid Usage (RAAU)
	-cu		Codon Usage (CU) (default)

-cutab

Tabulation of codon usage

-cutot

Tabulation of dataset’s codon usage

-rscu

Relative Synonymous Codon Usage (RSCU)

-fasta

fasta format

-tidy

fasta format

-reader

Reader format (codons are separated by spaces)

-transl

Conceptual translation of DNA to amino acid

-base

Detailed report of codon G+C composition

-dinuc

Dinucleotide usage of the three codon pos.

-noblk

No bulk output to be written to file

Some of the codonw subtools can be directly accessed using shortcuts prefixed with ’codonw-’.

AUTHOR

This manpage was written by Sascha Steinbiss for the Debian distribution and can be used for any other usage of the program.