Biobase.Infernal.Align

cmalign provides two interesting results, bit scores of sequences aligned to the model and the alignments themselves.

Documentation

data Align

cmalign results, includes sequence scores if available.

TODO stockholmAlignment, should be biostockholm (will be set after some fun iteratee tests). For now, the ByteString holds everything needed to parse using biostockholm.

Constructors

Align

Fields

modelIdentification :: ModelIdentification

sequenceScores :: [SequenceScore]

stockholmAlignment :: ByteString

data SequenceScore

Individual sequence scores.

TODO avgProbability should use Probability newtype

Constructors

SequenceScore

Fields

sequenceName :: !(ModelAccession, ModelIdentification, EmblAccession)

sequence name, typically RFxxxxxx;RfamID;embl-accession

sLength :: !Int

aligned sequence length

totalBitScore :: !BitScore

total alignment bitscore

structureBitScore :: !BitScore

structural score part

avgProbability :: !Double