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

letterTranslationTable :: TranslationTable Char Char -> TranslationTable (Letter DNA n) (Letter AA n)

Transform translation tables into the Letter DNA/Letter AA format.

Orphan instances

Translation (Codon (Letter DNA n))

Associated Types

type TargetType (Codon (Letter DNA n))

type CodonType (Codon (Letter DNA n))

type AAType (Codon (Letter DNA n))

Methods

translate :: TranslationTable (CodonType (Codon (Letter DNA n))) (AAType (Codon (Letter DNA n))) -> Codon (Letter DNA n) -> TargetType (Codon (Letter DNA n))

translateAllFrames :: TranslationTable (CodonType (Codon (Letter DNA n))) (AAType (Codon (Letter DNA n))) -> Codon (Letter DNA n) -> TargetType (Codon (Letter DNA n))

Translation (Primary DNA n)

Associated Types

type TargetType (Primary DNA n)

type CodonType (Primary DNA n)

type AAType (Primary DNA n)

Methods

translate :: TranslationTable (CodonType (Primary DNA n)) (AAType (Primary DNA n)) -> Primary DNA n -> TargetType (Primary DNA n)

translateAllFrames :: TranslationTable (CodonType (Primary DNA n)) (AAType (Primary DNA n)) -> Primary DNA n -> TargetType (Primary DNA n)