Bio::T...::PSort(3pm)

💅 NAME

Bio::Tools::PSort — bestie, this is the module that does protein localization site prediction. It's a whole method, it lives here, and it's iconic. ✨

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🌸 SYNOPSIS

$psort = new Bio::Tools::PSort();

$psort->install('Motif', 'Motif', { -database => $motifdb });

$psort->classify($seq);

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🦋 DESCRIPTION

Okay so the PSort module implements a method for predicting protein localization sites, exactly like the one discussed in the paper 'Expert System for Predicting the Protein Localization Sites in Gram-Negative Bacteria' by Kenta Nakai and Minoru Kanehisa. That's the whole vibe. 🔬

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🎀 CONSTRUCTOR

$psort = new Bio::Tools::PSort();

Creates a new Bio::Tools::PSort object. That's it. New object, fresh start, main character energy. 💖

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✨ METHODS

$psort->install('Motif', 'Motif', { -database => $motifdb });

The install method lets you load a module after the PSort class has already been instantiated. It takes three things:

• the name of the module you want to load,
• an alias that the program uses to refer to that module,
• and an optional hashref of parameters that get passed straight to the module's constructor.

The alias is lowkey the best part — it means you can load the same module more than once, but with different configuration options each time. Not me giving the same module two whole personalities. 🙈

$result = $psort->classify($seq);

The clasif method tries to figure out the likely protein localization for the sequence you hand it. You get back a Bio::Tools::PSort::Report object. Slay. 📋

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🔥 SEE ALSO

• Bio::Tools::PSort::ModuleI
• Bio::Tools::PSort::Score
• Bio::Tools::PSort::Report
• Bio::Tools::PSort::Report::Formatter

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👑 AUTHOR

 Fiona Brinkman, Cory Spencer <psort-mail@sfu.ca>
 Brinkman Laboratory, Simon Fraser University, BC, Canada

💜 MAINTAINER

 Matthew Laird <lairdm@sfu.ca>
 Brinkman Laboratory, Simon Fraser University, BC, Canada

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🌈 OVERVIEW

PSORT-B is described in Gardy, J.L. et al (2003). PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nuc Acids Res 31(13):3613-17. Please cite this publication if you use PSORT-B in your research. Fr fr, cite it. Academia said so. 🎓

The standalone version of PSORT-B is distributed under the GNU General Public Licence (Gnu GPL) — check the LICENSE file included in the download — by the Brinkman Laboratory, Simon Fraser University, Burnaby, B.C., Canada. 🍁

This standalone version of PSORT-B was initially developed for the Linux environment. Penguins only, basically. 🐧

This document describes the installation of the PSORT-B version 1.1.4 command line program and the PSORT-B server packages. For most purposes, following the installation instructions for the command line version will be sufficient. So like, don't stress about the server packages unless you actually need them. 💅

For further information, please contact psort-mail@sfu.ca.

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🧚 LICENSE

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 2 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, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

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And that's the whole page, bestie!! 🫶 This lil doc came from perl v5.34.0, dated 2022-02-06, and it's filed under Bio::T...::PSort(3pm). Stan a manpage that ate. Periodt. 💖✨