BiobaseXNA-0.5.3.0: Efficient RNA/DNA representations

Biobase.Secondary

Contents

Description

Secondary structure: define basepairs as Int-tuples, the three edges, a nucleotide can use for pairing and the cis/trans isomerism. Both edges and cis/trans come with a tag for unknown.

TODO set ext-annotations to be (isomerism,edge,edge) and have a asString instance to read cWW tSH and other notation.

Synopsis

Documentation

threeChar :: String -> ExtPairAnnotationSource

Easy reading of a three-Char string into a triple.

newtype Edge Source

Each nucleotide in a pair may be paired using one of three edges: watson-crik, sugar, or hoogsteen.

Constructors

Edge 

Fields

unEdge :: Int
 

Instances

Bounded Edge 
Enum Edge 
Eq Edge 
Ord Edge 
Read Edge

Human-readable Read instance.

Show Edge

Human-readable Show instance.

Ix Edge 
Prim Edge 
Unbox Edge 
Bounds Edge 
Vector Vector Edge 
MVector MVector Edge 
RemovePseudoKnots [ExtPairIdx] 
RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

MkD2Secondary (Int, [ExtPairIdx]) 

newtype CTisomerism Source

Nucleotides in a pairing may be in the cis(==?) or trans(==?) state.

Constructors

CT 

Fields

unCT :: Int
 

Instances

Instances for Edge

Instances for CTisomerism

Types

type PairIdx = (Int, Int)Source

A basepair is simply a pair of Ints which are 0-indexing a sequence.

TODO storable vector, newtype, peek/poke?

type Pair = (Nuc, Nuc)Source

A pair as a tuple containing Nucs.

type ExtPairAnnotation = (CTisomerism, Edge, Edge)Source

Annotation for a basepair.

type ExtPairIdx = (PairIdx, ExtPairAnnotation)Source

An extended basepair is a basepair, annotated with edge and CTisomerism.

type ExtPair = (Pair, ExtPairAnnotation)Source

An extended basepair, with nucleotides an annotation.

special show instances