Biobase.AAseq

This module has the translation tables for the genetic code.

Documentation

newtype AA

The amino acid newtype.

Constructors

AA

Fields

unAA :: Int

Instances

Enum AA

Eq AA

Ord AA

Read AA

Show AA

Ix AA

Prim AA

Unbox AA

Vector Vector AA

MVector MVector AA

MkAAseq [AA]

(Shape sh, Show sh, ExtShape sh) => ExtShape (:. sh AA)

(Shape sh, Show sh) => Shape (:. sh AA)

Creating functions and aa data.

aStop :: AA

aaRange :: [AA]

toAA :: Char -> AA

Translate Char amino acid representation into efficient AA newtype.

fromAA :: AA -> Char

Char representation of an AA.

class MkAAseq x where

Create amino acid sequences from different data sources.

Methods

mkAAseq :: x -> Vector AA

Instances

MkAAseq ByteString

MkAAseq ByteString

MkAAseq Text

MkAAseq [Char]

MkAAseq [AA]

MkAAseq (Vector Char)

type AAseq = Vector AA

primaryToAAseq :: Primary -> AAseq

Using the codon table, create an AAseq from the Primary sequence.

lookup tables

charAAList :: [(Char, AA)]

aACharList :: [(AA, Char)]

codonTable :: Map [Char] Char

nucCodonTable :: Map [Nuc] AA

instances