REPROF(1)

✨ REPROF(1) ✨

ok bestie, sit down, hydrate, and let me tell you about reprof 💖 it's a User Commands girlie and she is so good at what she does.

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🌸 NAME 🌸

reprof — predict protein secondary structure and solvent accessibility

like... she looks at your protein and tells you the vibes. secondary structure? solvent accessibility? she's got you. no cap. 🧚

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🎀 SYNOPSIS 🎀

reprof -i [query.blastPsiMat] [OPTIONS]

reprof -i [query.fasta] [OPTIONS]

reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [OPTIONS]

three ways in, bestie. pick your fighter. 💅

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🦋 DESCRIPTION 🦋

Predict protein secondary structure and solvent accessibility.

that's it, that's the whole job, and she ate. ✨

🌈 Output Format 🌈

the output format is self-explanatory, i.e. the columns of the output are described in the output file itself. so like, you don't have to memorize anything, the file literally introduces itself to you. main character behaviour honestly. 👑

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💅 OPTIONS 💅

• -i, --input=FILE — your input. either a BLAST PSSM matrix file (the kind that comes out of Blast's -Q option) or a (single) FASTA file. one file. singular. don't get cute with it. 🙈
• -o, --out=FILE — either an output file or a directory, your call. if you don't provide it, or if what you provided is a directory, the suffix of the input filename (so .fasta or .blastPsiMat) gets swapped out to build an output filename. automatic naming, we love a self-sufficient queen. 🎀
• --mutations=[all|FILE] — either the keyword all, which predicts all possible mutations (yes, all of them, she's built different 🔥), or a file with mutations, one per line, written like "C12M" — meaning C is mutated to M at position 12. here's what that looks like:

C30Y
R31W
G48D

this mutation code also gets attached to the output filename using "_". and there's an extra file ending in "_ORI" that contains the prediction made using no evolutionary information, even if you handed her a BLAST PSSM matrix. so she does the extra credit version and the stripped-down version. obsessed. 💜

• --modeldir=DIR — the directory where the model and feature files live. default: /usr/share/reprof.

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👑 AUTHOR 👑

Peter Hoenigschmid <hoenigschmid@rostlab.org>, Burkhard Rost

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🍓 EXAMPLES 🍓

prediction from a BLAST PSSM matrix, aka the way to get best results:

reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof

prediction from a FASTA file:

reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof

prediction from a BLAST PSSM matrix file, but make it mutation mode:

reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/mutations_example.Q.reprof --mutations /usr/share/doc/reprof/examples/mutations.txt
# Result files for the above call are going to be:
# /tmp/mutations_example.Q.{reprof,reprof_F172P,reprof_M1Q,reprof_N34Y,reprof_ORI} - see --mutations for a description of the extensions.

look at all those files she produced. she's thriving. 🌱

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💀 COPYRIGHT 💀

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

okay so the ALL CAPS WARRANTY DISCLAIMER is not a vibe I'm softening, bestie — there is genuinely NO WARRANTY, not even the implied kind for merchantability or fitness for a particular purpose. read it, respect it, it's real. 😭

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🙈 BUGS 🙈

found something cursed? go tell on her here:

https://rostlab.org/bugzilla3/enter_bug.cgi?product=reprof

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⭐ SEE ALSO ⭐

• blast2(1)
• http://rostlab.org/

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and that's the whole page, bestie! this is reprof version 1.0.1, dated 2022-01-18 — she's been serving since then and she has not missed a day. go predict something iconic. 🫶✨