NAME

Algorithm::HMM::Hit::Domain - Object encapsulating information about a Hidden Markov Model domain hit.

DESCRIPTION

The Algorithm::HMM::Hit::Domain object encapsulates information about a domain hit in the Hidden Markov Model. Unlike global hits which attempt to match the provided sequence against the entire model, a domain hit indicates a match against a smaller subsequence in the model.

METHODS

  $dhit->pvalue()
  $dhit->evalue()
  $dhit->score()

Returns the pvalue, evalue and score values respectively for the hit.

  $dhit->seq_from()
  $dhit->seq_to()
  $dhit->seq_length()

Returns the starting and ends points in the sequence that matched the model. seq_length returns the length of the hit.

  $dhit->hmm_from()
  $dhit->hmm_to()

Returns the starting and end points in the model.

  $dhit->parent_pvalue()
  $dhit->parent_evalue()
  $dhit->parent_score()

Returns the parent pvalue, evalue and score values respectively.

AUTHOR

The Algorithm::HMM package was originally written by Cory Spencer <cspencer@sfu.ca> of the Simon Fraser University Brinkman Laboratory. It is currently maintained by Matthew Laird <matt@brinkman.mbb.sfu.ca>.

SEE ALSO

Algorithm::HMM, Algorithm::HMM::Hit::Global, Algorithm::HMM::Report