Safe Haskell	None
Language	Haskell2010

Bio.Seq

Contents

Alphabet
Sequence types
DNA related functions

Synopsis

Alphabet

data Basic Source #

Alphabet defined by http://www.chem.qmul.ac.uk/iupac/ | Standard unambiguous alphabet

Instances

BioSeq RNA Basic Source #
Methods alphabet :: RNA Basic -> HashSet Char Source # fromBS :: ByteString -> RNA Basic Source #
BioSeq DNA Basic Source #
Methods alphabet :: DNA Basic -> HashSet Char Source # fromBS :: ByteString -> DNA Basic Source #

data IUPAC Source #

full IUPAC alphabet, including ambiguous letters

Instances

BioSeq DNA IUPAC Source #
Methods alphabet :: DNA IUPAC -> HashSet Char Source # fromBS :: ByteString -> DNA IUPAC Source #

data Ext Source #

extended alphabet

Instances

BioSeq DNA Ext Source #
Methods alphabet :: DNA Ext -> HashSet Char Source # fromBS :: ByteString -> DNA Ext Source #

Sequence types

data DNA alphabet Source #

DNA sequence

Instances

BioSeq' DNA Source #
Methods toBS :: DNA a -> ByteString Source # slice :: Int -> Int -> DNA a -> DNA a Source # length :: DNA a -> Int Source #
BioSeq DNA Ext Source #
Methods alphabet :: DNA Ext -> HashSet Char Source # fromBS :: ByteString -> DNA Ext Source #
BioSeq DNA IUPAC Source #
Methods alphabet :: DNA IUPAC -> HashSet Char Source # fromBS :: ByteString -> DNA IUPAC Source #
BioSeq DNA Basic Source #
Methods alphabet :: DNA Basic -> HashSet Char Source # fromBS :: ByteString -> DNA Basic Source #
Show (DNA a) Source #
Methods showsPrec :: Int -> DNA a -> ShowS # show :: DNA a -> String # showList :: [DNA a] -> ShowS #
Monoid (DNA a) Source #
Methods mempty :: DNA a # mappend :: DNA a -> DNA a -> DNA a # mconcat :: [DNA a] -> DNA a #

data RNA alphabet Source #

RNA sequence

Instances

BioSeq' RNA Source #
Methods toBS :: RNA a -> ByteString Source # slice :: Int -> Int -> RNA a -> RNA a Source # length :: RNA a -> Int Source #
BioSeq RNA Basic Source #
Methods alphabet :: RNA Basic -> HashSet Char Source # fromBS :: ByteString -> RNA Basic Source #

data Peptide alphabet Source #

Peptide sequence

Instances

BioSeq' Peptide Source #
Methods toBS :: Peptide a -> ByteString Source # slice :: Int -> Int -> Peptide a -> Peptide a Source # length :: Peptide a -> Int Source #

class BioSeq' s where Source #

Minimal complete definition

toBS, slice

Methods

toBS :: s a -> ByteString Source #

slice :: Int -> Int -> s a -> s a Source #

length :: s a -> Int Source #

Instances

BioSeq' Peptide Source #
Methods toBS :: Peptide a -> ByteString Source # slice :: Int -> Int -> Peptide a -> Peptide a Source # length :: Peptide a -> Int Source #
BioSeq' RNA Source #
Methods toBS :: RNA a -> ByteString Source # slice :: Int -> Int -> RNA a -> RNA a Source # length :: RNA a -> Int Source #
BioSeq' DNA Source #
Methods toBS :: DNA a -> ByteString Source # slice :: Int -> Int -> DNA a -> DNA a Source # length :: DNA a -> Int Source #

class BioSeq' s => BioSeq s a where Source #

Minimal complete definition

alphabet, fromBS

Methods

alphabet :: s a -> HashSet Char Source #

fromBS :: ByteString -> s a Source #

Instances

BioSeq RNA Basic Source #
Methods alphabet :: RNA Basic -> HashSet Char Source # fromBS :: ByteString -> RNA Basic Source #
BioSeq DNA Ext Source #
Methods alphabet :: DNA Ext -> HashSet Char Source # fromBS :: ByteString -> DNA Ext Source #
BioSeq DNA IUPAC Source #
Methods alphabet :: DNA IUPAC -> HashSet Char Source # fromBS :: ByteString -> DNA IUPAC Source #
BioSeq DNA Basic Source #
Methods alphabet :: DNA Basic -> HashSet Char Source # fromBS :: ByteString -> DNA Basic Source #

DNA related functions

rc :: DNA alphabet -> DNA alphabet Source #

O(n) Reverse complementary of DNA sequence.

gcContent :: DNA alphabet -> Double Source #

O(n) Compute GC content.

nucleotideFreq :: BioSeq DNA a => DNA a -> HashMap Char Int Source #

O(n) Compute single nucleotide frequency.