DEBIAN/SCORE_CONSERVATION(1)

DEBIAN/SCORE_CONSERVATION(1) 💖

okay bestie, welcome to the score_conservation(1) page from the Debian User Commands section — this is the one that goes hard on protein sequence conservation scoring, and yes we're gonna read the whole thing together 🫶

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✨ NAME ✨

score_conservation — score protein sequence conservation 🌸

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✨ SYNOPSIS ✨

score_conservation [options] ALIGNFILE

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✨ DESCRIPTION ✨

So basically: this tool scores protein sequence conservation in ALIGNFILE. And not to be that girl but ALIGNFILE has to be in FASTA, CLUSTAL or Stockholm format. Like, those are the only options, no negotiating 💅

Here are the conservation scoring methods that are implemented, all of them, no gatekeeping:

• sum of pairs
• weighted sum of pairs
• Shannon entropy
• Shannon entropy with property groupings (Mirny and Shakhnovich 1995, Valdar and Thornton 2001)
• relative entropy with property groupings (Williamson 1995)
• von Neumann entropy (Caffrey et al 2004)
• relative entropy (Samudrala and Wang 2006)
• Jensen-Shannon divergence (Capra and Singh 2007)

There's also a window-based extension — it folds the estimated conservation of sequentially adjacent residues into the score for each column. And the cute part? This window approach can be applied to any of the conservation scoring methods. versatility icon 👑

With default parameters, score_conservation(1) computes the conservation scores for the alignment using the Jensen-Shannon divergence and a window -w of 3. yes, default behaviour is already doing the most ✨

The sequence-specific output can be used as the conservation input for concavity(1). bestie crossover episode 🔥

And just so you know why you should care: conservation is highly predictive in identifying catalytic sites and residues near bound ligands. main character science fr fr 🧬

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✨ REFERENCES ✨

Capra JA and Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics, 23(15):1875-82, 2007.

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✨ OPTIONS ✨

• -a [NAME] — Reference sequence. Print scores in reference to the named sequence (ignoring gaps). Default prints the entire column. 🎯
• -b [0-1] — Lambda for the window heuristic linear combination. Default=.5.

Equation:

"score = (1 - lambda) * average_score_over_window_around_middle +
lambda * score_of_middle"

math girlies rise 🧮✨

• -d [FILE] — Background distribution file, e.g. distributions/swissprot.distribution. Default=built-in BLOSUM62.
• -g [0-1) — Gap cutoff. Do not score columns that contain more than gap cutoff fraction gaps. Default=.3. (and yes, the bracket situation in [0-1) is exactly what the original says, we don't editorialize 🫣)
• -h — Print help. the classic.
• -l [true|false] — Use sequence weighting. Default=true.
• -m [FILE] — Similarity matrix file, e.g. matrix/blosum62.bla or .qij. Default=matrix/blosum62.bla.

Some methods, e.g. js_divergence, do not use this. noted 📝

• -n [true|false] — Normalize scores. Print the z-score (over the alignment) of each column raw score. Default=false.
• -o FILE — Output file. Default: standard output stream. 📤
• -p [true|false] — Use gap penalty. Lower the score of columns that contain gaps, proportionally to the sum weight of the gapped sequences. Default=true.
• -s [METHOD] — Conservation estimation method, one of shannon_entropy property_entropy property_relative_entropy vn_entropy relative_entropy js_divergence sum_of_pairs. Default=js_divergence.
• -w [0-INT] — Window size. Number of residues on either side included in the window. Default=3.

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✨ EXAMPLES ✨

Note: you may have to copy and uncompress the example data files before running the following examples. lowkey annoying but it is what it is 🙈

Compute conservation scores for the alignment using the Jensen-Shannon divergence with default settings and print out the scores:

score_conservation /usr/share/doc/conservation-code/examples/2plc__hssp-filtered.aln

Score an alignment using Jensen-Shannon divergence, a window of size 3 (on either side of the residue), and the swissprot background distribution:

score_conservation -s js_divergence -w 3 -d \
 /usr/share/conservation-code/distributions/swissprot.distribution \
 /usr/share/doc/conservation-code/examples/2plc__hssp-filtered.aln

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✨ FILES ✨

Distributions

/usr/share/conservation-code/distributions

Matrices

/usr/share/conservation-code/matrix

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✨ SEE ALSO ✨

• Homepage <http://compbio.cs.princeton.edu/conservation/>
• Publication <http://bioinformatics.oxfordjournals.org/cgi/content/full/23/15/1875>
• concavity(1)

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and that's the whole page, bestie, no skips, no summarising, every single flag accounted for 💖✨

this one's version 20110309.0 and it's dated 2019-12-15, so when you cite it or check it later, that's the era you're in 🎀

go score some conservation, you're literally built for this 🦋👑