Biobase.Primary.Nuc.Conversion

Convert between different nucleotide representations

Single-character translations.

rnaTdna :: Letter RNA -> Letter DNA

Transform RNA to DNA. That means change U to T and keep the other characters as is.

dnaTrna :: Letter DNA -> Letter RNA

Transform DNA to RNA. That means change T to U and keep the other characters as is.

rnaGxna :: Letter RNA -> Letter XNA

Generalize an RNA character to a XNA character.

dnaGxna :: Letter DNA -> Letter XNA

Generalize a DNA character to a XNA character.

xnaSrna :: Letter XNA -> Letter RNA

Specialize XNA to RNA, T becomes N.

xnaSdna :: Letter XNA -> Letter DNA

Specialize XNA to DNA, U becomes N.

Reverse-complement of characters.

class Complement s t where

Produce the complement of a RNA or DNA sequence. Does intentionally not work for XNA sequences as it is not possible to uniquely translate A into either U or T.

Methods

complement :: s -> t

Instances

(Complement s t, Functor f) => Complement (f s) (f t)

(Complement s t, Unbox s, Unbox t) => Complement (Vector s) (Vector t)

Complement (Letter RNA) (Letter RNA)

Complement (Letter RNA) (Letter DNA)

Complement (Letter DNA) (Letter RNA)

Complement (Letter DNA) (Letter DNA)

transcribe :: Primary DNA -> Primary RNA

To transcribe a DNA sequence into RNA we reverse the complement of the sequence.