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PRESCOTT
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LICENSE.txt
MIT License
Copyright (c) 2018: Elodie Laine, Yasaman Karami and Alessandra Carbone.
Copyright (c) 2022-2023: Mustafa Tekpinar and Alessandra Carbone.
Permission is hereby granted, free of charge, to any person obtaining a copy
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README.md
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
# ![prescott logo](./images/logo-1.png)
# PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs
# A QUICK INTRODUCTION TO PRESCOTT (Population awaRe Epistatic and StruCtural mOdel of muTational effecTs)
## Introduction
PRESCOTT is a package predicting mutational effects in a protein based on population, evolutionary and structural information.
It is made up of two main programs: escott and prescott.
......@@ -75,5 +74,6 @@ Please note that the example input files for prescott are in the data directory
PRESCOTT is implemented in Python 3 and R. It has been tested only on Linux. Since PRESCOTT has many dependencies, we recommend using our web site or our docker image. If you are a determined user, you can find the steps required to install it from the source in the following link (or in the docs folder of this repository):
# Cite
Coming soon...
# Cite
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
docs/_build/html/analysis.html
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html"></a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html#prescott-population-aware-epistatic-and-structural-model-of-mutational-effects">PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs</a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html#cite">Cite</a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the ESCOTT Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#raw-escott-scores-and-their-interpretation">Raw ESCOTT Scores and Their Interpretation</a></li>
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docs/_build/html/introduction.html
......@@ -110,12 +110,11 @@ dependencies.</p>
<h3>Input Data Requirements for escott<a class="headerlink" href="#input-data-requirements-for-escott" title="Permalink to this heading"></a></h3>
<p>escott requires two files:</p>
<ul class="simple">
<li><p>a multiple sequence alignment (MSA) file in fasta format (mandatory):</p></li>
<li><p>a multiple sequence alignment (MSA) file in fasta format (mandatory):</p>
<ul>
<li><p>your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps.</p></li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Your</span> <span class="n">query</span> <span class="n">protein</span> <span class="n">must</span> <span class="n">be</span> <span class="n">the</span> <span class="n">first</span> <span class="n">sequence</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">fasta</span> <span class="n">file</span><span class="o">.</span> <span class="n">In</span> <span class="n">addition</span><span class="p">,</span> <span class="n">the</span> <span class="n">query</span> <span class="n">sequence</span> <span class="n">should</span> <span class="ow">not</span> <span class="n">contain</span> <span class="nb">any</span> <span class="n">gaps</span><span class="o">.</span>
</pre></div>
</div>
<ul class="simple">
</li>
<li><p>a structure file in PDB format (optional but highly recommended).</p></li>
</ul>
<p>One of the fastest ways to obtain both input MSA and a PDB file is to
......@@ -189,7 +188,7 @@ in the docs folder of this repository):</p>
</section>
<section id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2>
<p>Coming soon…</p>
<p>Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.</p>
</section>
</section>
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docs/_build/latex/prescott.fdb_latexmk
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docs/_build/latex/prescott.log
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 10 OCT 2023 17:38
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Chapter 2.
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Chapter 3.
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(rerunfilecheck) Checksum: 8119393C8F110FFBB217A1E7B2C390DE;6307.
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docs/_build/latex/prescott.tex
......@@ -61,7 +61,7 @@
\title{prescott}
\date{Oct 10, 2023}
\date{Oct 24, 2023}
\release{1.5.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
......@@ -115,13 +115,13 @@ escott requires two files:
\item {}
\sphinxAtStartPar
a multiple sequence alignment (MSA) file in fasta format (mandatory):
\begin{itemize}
\item {}
\sphinxAtStartPar
your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps.
\end{itemize}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n}{Your} \PYG{n}{query} \PYG{n}{protein} \PYG{n}{must} \PYG{n}{be} \PYG{n}{the} \PYG{n}{first} \PYG{n}{sequence} \PYG{o+ow}{in} \PYG{n}{the} \PYG{n}{fasta} \PYG{n}{file}\PYG{o}{.} \PYG{n}{In} \PYG{n}{addition}\PYG{p}{,} \PYG{n}{the} \PYG{n}{query} \PYG{n}{sequence} \PYG{n}{should} \PYG{o+ow}{not} \PYG{n}{contain} \PYG{n+nb}{any} \PYG{n}{gaps}\PYG{o}{.}
\end{sphinxVerbatim}
\begin{itemize}
\item {}
\sphinxAtStartPar
a structure file in PDB format (optional but highly recommended).
......@@ -242,7 +242,7 @@ in the docs folder of this repository):
\section{Citation}
\label{\detokenize{introduction:citation}}
\sphinxAtStartPar
Coming soon…
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
\sphinxstepscope
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docs/introduction.rst
......@@ -25,9 +25,7 @@ escott requires two files:
* a multiple sequence alignment (MSA) file in fasta format (mandatory):
::
Your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps.
* your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps.
* a structure file in PDB format (optional but highly recommended).
......@@ -120,7 +118,7 @@ in the docs folder of this repository):
Citation
--------
Coming soon…
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
.. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
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