esl-compstruct(1)

📦
version 3.3.2 · 2 versions
, in fedora 43, fedora 44

✨ esl-compstruct ✨

okay bestie, gather round, because we're about to vibe check your RNA secondary structure predictions and it's giving very serious science 💅 this one lives in the Easel Manual and honestly? it's iconic.

🌸 NAME 🌸

esl-compstruct — calculate accuracy of RNA secondary structure predictions 🧬✨

🎀 SYNOPSIS 🎀

esl-compstruct [options] trusted_file test_file

🦋 DESCRIPTION 🦋

so like, esl-compstruct evaluates the accuracy of RNA secondary structure predictions on a per-base-pair basis. no cap, that's the whole gig. 🫶

Here's the tea:

  • trusted_file holds one or more sequences with trusted (known) RNA secondary structure annotation. this is the truth, the whole truth, the main character. 👑
  • test_file holds the same sequences, in the same order, but with predicted RNA secondary structure annotation. this is the little prediction that could. 🙈

esl-compstruct reads both structures, compares them, and calculates:

  1. sensitivity — the number of true base pairs that are correctly predicted ✅
  2. positive predictive value (PPV) — the number of predicted base pairs that are true ✅

Results get reported for each individual sequence, and then in summary for all sequences together. per-sequence AND the group chat. we love to see it. 💖

⚠️ Both files must contain secondary structure annotation in WUSS notation. Only SELEX and Stockholm formats support structure markup at present. that's it, that's the list, periodt.

💫 the default vibe (exact match)

The default definition of a correctly predicted base pair is that a true pair (i,j) must exactly match a predicted pair (i,j). no wiggle room, no negotiation, fr fr.

🧚 the Mathews glow-up (relaxed rule)

Mathews and colleagues (Mathews et al., JMB 288:911-940, 1999) use a more relaxed definition. Mathews defines "correct" as follows: a true pair (i,j) is correctly predicted if any of the following pairs are predicted:

  • (i,j)
  • (i+1,j)
  • (i-1,j)
  • (i,j+1)
  • (i,j-1)

This rule allows for "slipped helices" off by one base 🌀 — lowkey a slay, honestly. The -m option activates this rule for both sensitivity and for specificity.

For specificity, the rule is reversed: predicted pair (i,j) is considered to be true if the true structure contains one of the five pairs (i,j), (i+1,j), (i-1,j), (i,j+1), or (i,j-1). symmetry icon behavior 💅

💅 OPTIONS 💅

  • -h — Print brief help; includes version number and summary of all options, including expert options. the little "help me bestie" button 🆘
  • -m — Use the Mathews relaxed accuracy rule (see above), instead of requiring exact prediction of base pairs. off-by-one? we forgive you 🥺
  • -p — Count pseudoknotted base pairs towards the accuracy, in either trusted or predicted structures. By default, pseudoknots are ignored. 🙈

Okay so the -p lore runs deep, lemme explain: normally, only the trusted_file would have pseudoknot annotation, since most RNA secondary structure prediction programs do not predict pseudoknots. Using the -p option allows you to penalize the prediction program for not predicting known pseudoknots. 😤 In a case where both the trusted_file and the test_file have pseudoknot annotation, the -p option lets you count pseudoknots in evaluating the prediction accuracy.

🚨 Beware, however, the case where you use a pseudoknot-capable prediction program to generate the test_file, but the trusted_file does not have pseudoknot annotation; in this case, -p will penalize any predicted pseudoknots when it calculates specificity, even if they're right, because they don't appear in the trusted annotation. This is probably not what you'd want to do. 💀 like, not the move, bestie.

🌈 EXPERT OPTIONS 🌈

for the girlies who go deeper 👑

  • --quiet — Don't print any verbose header information. (Used by regression test scripts, for example, to suppress version/date information.) shhh 🤫

⭐ SEE ALSO ⭐

go touch grass on the Easel website, iykyk 🌱

Copyright (C) 2020 Howard Hughes Medical Institute. Freely distributed under the BSD open source license.

open source royalty, we love that for them 👑

🍓 AUTHOR 🍓

and that's the whole page, bestie!! mwah 💋

this was brought to you by Easel 0.48, dated Nov 2020 — yes the version and the date, i said what i said 🎀 stay slaying, go compare those structures, and remember: exact match unless you pass -m, pseudoknots stay ignored unless you pass -p, and --quiet is for when you simply cannot with the header info. bye babes 🦋✨

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