Bio.SeqLoc.Strand

Utilities for manipulating nucleotide sequences and locations on nucleotide sequences that occur on a forward or a reverse-complement strand.

Documentation

data Strand :: *

A Strand is either plus (forward) or minus (reverse or reverse-complement)

Constructors

Plus

Minus

Instances

Eq Strand

Ord Strand

Read Strand

Show Strand

LocRepr Strand

Stranded Strand

Typeable * Strand

compl :: Char -> Char

Complement of a nucleotide character, swap AT and GC preserving case and leave all other characters unchanged.

class Stranded s where

A nucleotide sequence or location on a nucleotide sequence that lies on a specific strand and has an orientation.

Methods

revCompl :: s -> s

Instances

Stranded Char

Stranded Word8

Stranded String

Stranded ByteString

Stranded ByteString

Stranded Strand

Stranded Pos

Stranded ContigLoc

Stranded SpliceLoc

Stranded s => Stranded (OnSeq s)

stranded :: Stranded s => Strand -> s -> s

Convert the orientation of a Stranded thing based on a specified Strand