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Get Codon and Bicodon frequency (version 0.1.2)

Source for Sequence Data:

FASTA nucleotide sequences:

Taxonomy ID to list in output:

9606 is Homo sapiens (human)

Organelle to list in output:

genomic is default

Division to list in output:

custom is default

Assembly to list in output:

hg38 is default

Species to list in output:

Homo sapiens is default

Translation table:

Calculate Codon and Bicodon (Codon Pair) usage frequency from FASTA files.

Output is designed to mimic that from CoCoPUTs (https://dnahive.fda.gov/dna.cgi?cmd=codon_usage&id=537&mode=cocoputs; e.g. https://dnahive.fda.gov/dna.cgi?cmd=objFile&ids=537&filename=Refseq_Bicod.tsv&raw=1).

Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).

Example of CoCoPUTs style codon output, the majority of codons have been removed in this example, for brevity:

Division Assembly Taxid Species Organelle Translation Table # CDS # Codons aaa aac aag aat ...

custom hg38 9606 Homo sapiens genomic 1 4 859 14 13 29 8 ...

Division	Assembly	Taxid	Species	Organelle	Translation Table	# CDS	# Codons	aaa	aac	aag	aat	...
custom	hg38	9606	Homo sapiens	genomic	1	4	859	14	13	29	8	...

Example of CoCoPUTs style bicodon output, the majority of bicodons (codon pairs) have been removed in this example, for brevity:

Division Assembly Taxid Species Organelle Translation Table # CDS # Codon Pairs aaaaaa aaaaac aaaaag aaaaat ...

custom hg38 9606 Homo sapiens genomic 1 4 859 0 0 0 1 ...