Safe Haskell	None
Language	Haskell2010

Biobase.GeneticCodes.Translation

Description

Abstract translation functionality. Given a genetic code translation table (as provided within this module), provide translation from the nucleotide to the amino acid alphabet.

Limited "backtranslation" capabilities are provided. Since this process is lossy, it should only be used in very specific circumstances.

TODO Translation from @BioSequence RNA is missing.

Synopsis

class Translation t where
- type TargetType t :: *
- type CodonType t :: *
- type AAType t :: *
- translate :: TranslationTable (CodonType t) (AAType t) -> t -> TargetType t

Documentation

class Translation t where Source #

Associated Types

type TargetType t :: * Source #

Defines the target type for a given translation input.

type CodonType t :: * Source #

Type of the nucleotide characters.

type AAType t :: * Source #

Type of the amino acid characters.

Methods

translate :: TranslationTable (CodonType t) (AAType t) -> t -> TargetType t Source #

Translate from a given type of sequence t into the target type.

Instances

Translation String Source #	Strings of characters are normally very inconvenient but useful in backtracking cases. Fully assumes that the alphabet is DNA. Ignores non-triplets at the end.
Instance details Defined in Biobase.GeneticCodes.Translation Associated Types type TargetType String :: Type Source # type CodonType String :: Type Source # type AAType String :: Type Source # Methods translate :: TranslationTable (CodonType String) (AAType String) -> String -> TargetType String Source #
Translation (Codon Char) Source #	Very simple translation of individual base triplets.
Instance details Defined in Biobase.GeneticCodes.Translation Associated Types type TargetType (Codon Char) :: Type Source # type CodonType (Codon Char) :: Type Source # type AAType (Codon Char) :: Type Source # Methods translate :: TranslationTable (CodonType (Codon Char)) (AAType (Codon Char)) -> Codon Char -> TargetType (Codon Char) Source #
Translation (BioSequence DNA) Source #	Translation of `BioSequence DNA`. The translation tables assume DNA triplets anyway. Biologically there should be a transcription step in between. Ignores non-triplets at the end.
Instance details Defined in Biobase.GeneticCodes.Translation Associated Types type TargetType (BioSequence DNA) :: Type Source # type CodonType (BioSequence DNA) :: Type Source # type AAType (BioSequence DNA) :: Type Source # Methods translate :: TranslationTable (CodonType (BioSequence DNA)) (AAType (BioSequence DNA)) -> BioSequence DNA -> TargetType (BioSequence DNA) Source #