bioinformatics-toolkit-0.10.0: A collection of bioinformatics tools
Safe HaskellNone
LanguageHaskell2010

Bio.Seq

Synopsis

Alphabet

data Basic Source #

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

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Instances details
BioSeq RNA Basic Source # 
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Defined in Bio.Seq

BioSeq DNA Basic Source # 
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Defined in Bio.Seq

data IUPAC Source #

full IUPAC alphabet, including ambiguous letters

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BioSeq DNA IUPAC Source # 
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data Ext Source #

extended alphabet

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BioSeq DNA Ext Source # 
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Sequence types

data DNA alphabet Source #

DNA sequence

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BioSeq' DNA Source # 
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Defined in Bio.Seq

BioSeq DNA Ext Source # 
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BioSeq DNA IUPAC Source # 
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BioSeq DNA Basic Source # 
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Show (DNA a) Source # 
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Methods

showsPrec :: Int -> DNA a -> ShowS #

show :: DNA a -> String #

showList :: [DNA a] -> ShowS #

Semigroup (DNA a) Source # 
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Defined in Bio.Seq

Methods

(<>) :: DNA a -> DNA a -> DNA a #

sconcat :: NonEmpty (DNA a) -> DNA a #

stimes :: Integral b => b -> DNA a -> DNA a #

Monoid (DNA a) Source # 
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Defined in Bio.Seq

Methods

mempty :: DNA a #

mappend :: DNA a -> DNA a -> DNA a #

mconcat :: [DNA a] -> DNA a #

data RNA alphabet Source #

RNA sequence

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BioSeq' RNA Source # 
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BioSeq RNA Basic Source # 
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data Peptide alphabet Source #

Peptide sequence

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BioSeq' Peptide Source # 
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class BioSeq' s where Source #

Minimal complete definition

toBS, slice, unsafeFromBS

Methods

toBS :: s a -> ByteString Source #

unsafeFromBS :: ByteString -> s a Source #

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

length :: s a -> Int Source #

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BioSeq' Peptide Source # 
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BioSeq' RNA Source # 
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BioSeq' DNA Source # 
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class BioSeq' seq => BioSeq seq alphabet where Source #

Minimal complete definition

alphabet

Methods

alphabet :: Proxy (seq alphabet) -> HashSet Char Source #

fromBS :: ByteString -> Either String (seq alphabet) Source #

Instances

Instances details
BioSeq RNA Basic Source # 
Instance details

Defined in Bio.Seq

BioSeq DNA Ext Source # 
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Defined in Bio.Seq

BioSeq DNA IUPAC Source # 
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Defined in Bio.Seq

BioSeq DNA Basic Source # 
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Defined in Bio.Seq

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

O(n) Compute single nucleotide frequency.