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

writeSangerQ

hReadSangerQ

hWriteSangerQ

readIllumina

writeIllumina

hReadIllumina

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