Biobase.Primary.Trans

This module provides functionality for translation between nucleotides and amino acids.

NOTE aaDNAseq is lossy. Might be a good idea to consider something more involved?

TODO we need different functions, depending on if we have a part of a genome in DNA form, or some messenger RNA. It'll probably also be useful to return Either, with Left indicating error like partially translated sequence due to intermediate stop codons, or so.

TODO dnaAAseq and aaDNAseq can be nicely optimized using flatten and friends.

Documentation

dnaAAseq :: Primary DNA -> Primary AA

Using the codon table, create an amino acid sequence from a DNA sequence (encoded as 'Primary DNA'). Suffixed seq as we deal with sequences, not letters.

aaDNAseq :: Primary AA -> Primary DNA

Transform an amino acid sequence back into DNA.

WARNING: This is lossy!

Embedded codon data

aaDNAmap :: Map (Letter AA) (Primary DNA)

Lossy backtransformation.

dnaAAmap :: Map (Primary DNA) (Letter AA)

codonTable :: Map String Char

codonListEmbedded :: ByteString

Raw codon table