---
name: "Algorithm::HMM::Hit::Domain"
section: "3pm"
platform: "linux"
package: "psortb"
version: "3.0.6+dfsg-4+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Algorithm::HMM::Hit::Domain"
---

# Algorithm::HMM::Hit::Domain(3pm)

Object encapsulating information about a Hidden Markov Model domain hit.

## 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