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PRESCOTT
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LICENSE.txt
MIT License MIT License
Copyright (c) 2018: Elodie Laine, Yasaman Karami and Alessandra Carbone.
Copyright (c) 2022-2023: Mustafa Tekpinar 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 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) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
# ![prescott logo](./images/logo-1.png) # ![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. 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. 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 ...@@ -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): 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 # Cite
Coming soon... Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
docs/_build/html/analysis.html
...@@ -44,9 +44,7 @@ ...@@ -44,9 +44,7 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> </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> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current"> <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">Introduction</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="docker.html">Using ESCOTT via Docker</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-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> <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> ...@@ -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> <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> <p>escott requires two files:</p>
<ul class="simple"> <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> </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> </li>
</pre></div>
</div>
<ul class="simple">
<li><p>a structure file in PDB format (optional but highly recommended).</p></li> <li><p>a structure file in PDB format (optional but highly recommended).</p></li>
</ul> </ul>
<p>One of the fastest ways to obtain both input MSA and a PDB file is to <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> ...@@ -189,7 +188,7 @@ in the docs folder of this repository):</p>
</section> </section>
<section id="citation"> <section id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2> <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>
</section> </section>
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\ No newline at end of file \ No newline at end of file
docs/_build/latex/prescott.fdb_latexmk
# Fdb version 3 # Fdb version 3
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(generated) (generated)
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"prescott.ind" "prescott.ind"
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...@@ -140,13 +140,13 @@ ...@@ -140,13 +140,13 @@
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...@@ -161,7 +161,7 @@ ...@@ -161,7 +161,7 @@
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......
docs/_build/latex/prescott.log
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Chapter 2. Chapter 2.
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Chapter 3. Chapter 3.
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docs/_build/latex/prescott.tex
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
\title{prescott} \title{prescott}
\date{Oct 10, 2023} \date{Oct 24, 2023}
\release{1.5.0} \release{1.5.0}
\author{Mustafa Tekpinar} \author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}} \newcommand{\sphinxlogo}{\vbox{}}
...@@ -115,13 +115,13 @@ escott requires two files: ...@@ -115,13 +115,13 @@ escott requires two files:
\item {} \item {}
\sphinxAtStartPar \sphinxAtStartPar
a multiple sequence alignment (MSA) file in fasta format (mandatory): 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} \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 {} \item {}
\sphinxAtStartPar \sphinxAtStartPar
a structure file in PDB format (optional but highly recommended). a structure file in PDB format (optional but highly recommended).
...@@ -242,7 +242,7 @@ in the docs folder of this repository): ...@@ -242,7 +242,7 @@ in the docs folder of this repository):
\section{Citation} \section{Citation}
\label{\detokenize{introduction:citation}} \label{\detokenize{introduction:citation}}
\sphinxAtStartPar \sphinxAtStartPar
Coming soon… Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
\sphinxstepscope \sphinxstepscope
......
docs/introduction.rst
...@@ -25,9 +25,7 @@ escott requires two files: ...@@ -25,9 +25,7 @@ escott requires two files:
* a multiple sequence alignment (MSA) file in fasta format (mandatory): * 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). * a structure file in PDB format (optional but highly recommended).
...@@ -120,7 +118,7 @@ in the docs folder of this repository): ...@@ -120,7 +118,7 @@ in the docs folder of this repository):
Citation 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 .. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT :target: https://opensource.org/licenses/MIT
......
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