Algori...:Domain(3pm)

✨ NAME ✨

Algorithm::HMM::Hit::Domain — the little object that holds all the tea about a Hidden Markov Model domain hit 🧬💅

So like, the manual name is Algori...:Domain(3pm) (she got truncated at the party, we still love her) and she's part of the Algorithm::HMM friend group, no biggie.

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💖 DESCRIPTION 💖

okay bestie, listen up, because this is the whole vibe 🫶

The Algorithm::HMM::Hit::Domain object is literally just a container that encapsulates information about a domain hit in the Hidden Markov Model. That's it. That's the job. She's holding the receipts 📦✨

Now here's the part that matters — and I need you to lock in for this one — domain hits are NOT the same as global hits. Global hits try to match your provided sequence against the entire model. Main character energy, wants the whole thing. But a domain hit? A domain hit indicates a match against a smaller subsequence in the model. She's focused. She's selective. She found her niche and she ATE 💅🔥

So like, one wants the full picture, the other just wants that one perfect little fragment. Both valid. Both iconic. Just different 🦋

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🌸 METHODS 🌸

🌈 the stats girlies

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

Returns the pvalue, evalue and score values respectively for the hit. Respectively!! In that order!! Don't mix them up or it's gonna be giving chaos 😭

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🎀 where it matched in your sequence

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

Returns the starting and ending points in the sequence that matched the model. And seq_length returns the length of the hit. So like, seq_from is where it starts, seq_to is where it ends, and seq_length is how long the whole situation is. Math, but make it cute 📏✨

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🧚 where it matched in the model

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

Returns the starting and end points in the model. That's it, that's the whole method, no notes 💜

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👑 the parent info

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

Returns the parent pvalue, evalue and score values respectively. Yes, respectively again. The parent said "I raised you" and honestly? She did 🌟

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🦋 AUTHOR 🦋

The Algorithm::HMM package was originally written by Cory Spencer <cspencer@sfu.ca> of the Simon Fraser University Brinkman Laboratory. She's currently maintained by Matthew Laird <matt@brinkman.mbb.sfu.ca>. Shoutout to the maintainers fr fr, they keep the lights on 🫶🔥

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⭐ SEE ALSO ⭐

• Algorithm::HMM
• Algorithm::HMM::Hit::Global
• Algorithm::HMM::Report

go read those too, they're all connected, iykyk 🌈

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okay that's the whole page, ily, go match some domains 💖

sign-off time: this lil doc is from perl v5.34.0, dated 2022-02-06, and the page header says Algori...:Domain(3pm) because someone really said "let's truncate it, it'll be fine" and honestly? It was not fine but we move 💀✨