BiobaseInfernal-0.5.3.0: Infernal data structures and tools

Biobase.Infernal

Description

Re-export the most import parts.

Synopsis

Documentation

eneeTabularHit :: (Functor m, Monad m) => Enumeratee ByteString [TabularHit] m aSource

Transform a stream into tabular hits.

data VerboseHit Source

Captures a complete alignment

Constructors

VerboseHit 

Fields

vhTarget :: (Int, Int)

part of target sequence (start counting at 1)

vhQuery :: (Int, Int)

which part of the CM/stk do we align to

vhCM :: ByteString

the CM for this alignment

vhStrand :: Strand

should be either + or -

vhScore :: Double

bit score

vhEvalue :: Double

number of hits we expect to find with score or higher for targetSequence length

vhPvalue :: Double

?

vhGC :: Int

?

vhScaffold :: ByteString

scaffold, chromosome, ... (the name of the sequence, not the sequence data!)

vhWuss :: ByteString

fancy secondary structure annotation using wuss notation

vhConsensus :: ByteString

query consensus (upper: highly, lower: weak/no)

vhScoring :: ByteString

represents where positive and negative scores come from

vhSequence :: ByteString

the target sequence which aligns to the model

eneeVerboseHit :: (Functor m, Monad m) => Enumeratee ByteString [VerboseHit] m aSource

Transforms a stream into verbose hits. We need to keep a state in the accumulator to keep track of the current CM, scaffold and strand.

data Species Source

For each species, we store the name and a classification list from most general (head) to most specific (last). The database comes with the NCBI taxon identifier (taxid).

Constructors

Species 

Instances

data Clan Source

Simple RfamClan data wrapper. Could Easily be just a list of bytestrings, which it is using strings

Instances