BiobaseInfernal- Infernal data structures and tools




data VerboseHit Source

Captures a complete alignment




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

vhAnnotation :: ![ByteString]

any annotations that could be associated (# lines)