Bio.Sequence

Data structures etc (Bio.Sequence.SeqData)

data Sequence t

data Unknown

type Offset

type SeqData

type Qual

type QualData

Accessor functions

seqlength

seqlabel

seqheader

seqdata

seqqual

(!)

appendHeader

setHeader

Converting to and from String.

fromStr

toStr

Nucleotide functionality.

compl

revcompl

revcompl'

data Nuc

castToNuc

Protein sequence functionality

data Amino

translate

fromIUPAC

toIUPAC

castToAmino

Other utility functions

defragSeq

seqmap

File IO

Generic sequence reading

readNuc

readProt

The Fasta file format (Bio.Sequence.Fasta)

readFasta

hReadFasta

writeFasta

hWriteFasta

Quality data

readQual

writeQual

hWriteQual

readFastaQual

writeFastaQual

hWriteFastaQual

The FastQ format (Bio.Sequence.FastQ)

readFastQ

writeFastQ

hReadFastQ

hWriteFastQ

readSangerQ

readIllumina

writeSangerQ

writeIllumina

hReadSangerQ

hReadIllumina

hWriteSangerQ

hWriteIllumina

The phd file format (Bio.Sequence.Phd)

readPhd

hReadPhd

TwoBit file format support (Bio.Seqeunce.TwoBit)

decode2Bit

read2Bit

hRead2Bit

Hashing functionality (Bio.Sequence.HashWord)

data HashF k

contigous

rcontig

rcpacked

Entropy calculations

class KWords s

entropy