PROFTMB(1)

📦
version 1.1.12 · 3 versions
, in debian bookworm, ubuntu jammy, ubuntu noble

💅 PROFTMB — the girlies' guide to proftmb 💅

okay bestie, sit DOWN, because this one's a User Commands classic and it's genuinely so cool. this is the manual page for proftmb, and I'm about to make it make sense. no cap. 🫶

✨ NAME ✨

proftmb — per-residue prediction of bacterial transmembrane beta barrels 🦠🛢️

like, it looks at a sequence and tells you, residue by residue, where the membrane-y bits are. it's giving structural biology but make it slay.

🌸 SYNOPSIS 🌸

proftmb [options]

that's it. that's the whole vibe. you just feed it options and it goes. 🎀

💖 DESCRIPTION 💖

proftmb predicts bacterial transmembrane beta barrels from sequence using profile fed Hidden Markov Models (HMM). yes, that's a real sentence, and yes, HMMs are iconic. 🧚

🦋 Output format 🦋

bestie it's self-annotating. the letters it spits out mean this, and you WILL need to know them:

  • i — inside cytoplasm
  • O — outside cytoplasm</outside> (as written: outside cytoplasm)
  • U — up (on chain moving out of cytoplasm)
  • D — down (on chain moving into cytoplasm)

memorise those four and you're literally set. 💅

📚 References 📚

Bigelow, H. and Rost, B. (2006). PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res, 34(Web Server issue), W186-8.

go cite it, academic bestie. 👑

🎀 To invoke the menu, type:

proftmb --menu

yes girl, there's a whole menu. you don't have to memorise the flags if you don't want to (but I'm about to give you all of them anyway, because we don't gatekeep here). 🌈

⭐ The options are:

  • -d, --directory-root <STRING> — the root path where the files for options -s, -r, -l, -a, -e, -t, -u, -z, -n live. one home base for the whole crew. 🏠
  • -a, --reduction-state-decode <STRING> — state reduction for decoding. 🧬
  • -b, --reduction-state-report <STRING> — state reduction for reporting. 📝
  • -m, --membrane-strand-states <STRING> — list of membrane strand states. 🌊
  • -z, --z-curve-file <STRING> — file containing means and sd's at integral length values. 📈
  • -x, --z-calibration-curve <STRING> — file mapping coverage and accuracy values to z-scores. 🎯
  • -n, --null-frequency <STRING> — background frequency file. 📊
  • -c, --minimum-score-cutoff <DOUBLE> — minimum z-score for per-residue prediction. anything below this just doesn't make the cut, sorry babe. ✂️
  • -o, --outfile-prefix <STRING> — output file prefix for the three files generated: PREFIX_dat.txt, PREFIX_proftmb_pretty.txt, PREFIX_proftmb_tabular.txt. three files, one prefix, very efficient of it. 💅
  • -s, --static-model-data <STRING> — data representing the model architecture. 🏗️
  • -t, --trained-params <STRING> — params representing the encoded training data. 🧠
  • -q, --test-blastQ-file-or-dir <STRING> — psiblast profile (-Q) or directory (full pathname or relative to current directory) with many profiles. the input moment fr fr. 📥
  • -w, --single-sequence-name <STRING> — if the -q option points to a single file, this is the name. one file, one name, iconic. 🏷️
  • -v, --list-blastQ-files <STRING> — list of psiblast files to process in directory (leave blank to process all files). blank = everything. no thoughts, head empty, process it all. 🌈
  • --outfile-pretty <STRING> — pretty output file (overrides automatic name PREFIX_proftmb_pretty.txt). 💖
  • --outfile-tab <STRING> — tabulated output file (overrides automatic name PREFIX_proftmb_tabular.txt). 📋
  • --outfile-dat <STRING> — data output file (overrides automatic name PREFIX_dat.txt). 🗂️
  • --version <BOOL> — output version information and exit. bye bestie 👋
  • --quiet <BOOL> — be quiet. 🤫 (respectfully. sometimes you just need peace.)
lowkey important: --outfile-pretty, --outfile-tab and --outfile-dat each override the automatic name they'd otherwise get from the prefix. so if you set them, that's the name you get, periodt.

💀 BUGS 💀

Please report bugs at https://rostlab.org/bugzilla3/enter_bug.cgi?product=proftmb.

not me telling you where to file the bugs 😭 do it anyway, the devs wanna know. 🫶

🔥 EXAMPLES 🔥

proftmb @/usr/share/proftmb/options -q /usr/share/doc/proftmb/examples/example.Q -o /tmp/example

The above produces 3 output files: /tmp/example_proftmb_tabular.txt, /tmp/example_proftmb_pretty.txt and /tmp/example_dat.txt. Compare these to the examples in /usr/share/doc/proftmb/examples.

three files out of one command?? she ATE. 👑 compare them, vibe check them, make sure everything lines up. ✨

Copyright © 2004 Henry Bigelow

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 package 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 that's the whole page bestie, you're officially educated 💜 this was proftmb version 1.1.12, dated January 2022 — go predict some beta barrels and slay. 🦋🎀✨

📦 where this page comes from