BiobaseInfernal- Infernal data structures and tools



Re-export the most import parts.



data TabularHit Source

Tabular Infernal hits. See Biobase.Infernal.Hit for description of the individual fields.


Read TabularHit 
Show TabularHit 
Hit TabularHit

Generalized accessors.

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

Transform a stream into tabular hits.

data VerboseHit Source

Captures a complete alignment




vhTargetStart :: !Int

part of target sequence (start counting at 1)

vhTargetStop :: !Int
vhModelStart :: !Int

which part of the CM/stk do we align to

vhModelStop :: !Int

which part of the CM/stk do we align to

vhModel :: !ModelIdentification

the CM for this alignment

vhStrand :: !Strand

should be either + or -

vhBitScore :: !BitScore

bit score

vhEvalue :: !Double

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

vhPvalue :: !Double


vhGCpercent :: !Int


vhTarget :: !Scaffold

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

vhAnnotation :: ![ByteString]

any annotations that could be associated (# lines)


Read VerboseHit 
Show VerboseHit 
Hit VerboseHit

Generalized accessors.

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 SpeciesTaxonomy 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).

data Clan Source

Simple Rfam clan data.




cAccession :: !ClanAccession

result of the AC CL00001 line, keeping 1 in this case.

cIdentifier :: !ClanIdentification

the ID tRNA line, keeping tRNA.

cMembers :: ![ModelAccession]

all the MB RF00005;, MB RF00023; lines, keeping [5,23].

cStrings :: ![ByteString]

all lines of each clan, without any processing (except being in lines).