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title: Iterative_masking


keywords: fastai
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summary: "Supporting repository for: "Generative power of a protein language model trained on multiple sequence alignments" (preprint: https://doi.org/10.1101/2022.04.14.488405). We use MSA Transformer (https://doi.org/10.1101/2021.02.12.430858) to generate synthetic protein sequences by masking iteratively the same MSA."
description: "Supporting repository for: "Generative power of a protein language model trained on multiple sequence alignments" (preprint: https://doi.org/10.1101/2022.04.14.488405). We use MSA Transformer (https://doi.org/10.1101/2021.02.12.430858) to generate synthetic protein sequences by masking iteratively the same MSA."
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<h2 id="Getting-started">Getting started<a class="anchor-link" href="#Getting-started"> </a></h2><p>Clone this repository on your local machine by running:</p>
<div class="highlight"><pre><span></span>git clone git@github.com:Bitbol-Lab/Iterative_masking.git
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<p>and move inside the root folder.
One can the use directly the functions from the cloned repository (in the folder <code>Iterative_masking</code>) or install it with an editable install running:</p>
<div class="highlight"><pre><span></span>pip install -e .
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<p>We recommend creating and activating a dedicated <code>conda</code> or <code>virtualenv</code> Python virtual environment.</p>
<h2 id="Requirements">Requirements<a class="anchor-link" href="#Requirements"> </a></h2><p>In order to use the functions, the following python packages are required:</p>
<ul>
<li>numpy</li>
<li>scipy</li>
<li>numba</li>
<li>fastcore</li>
<li>biopython</li>
<li>esm==0.4.0</li>
<li>pytorch</li>
</ul>
<p>It is also required to use a GPU (with cuda).</p>

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<h2 id="How-to-use">How to use<a class="anchor-link" href="#How-to-use"> </a></h2>
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<p><a href="/Iterative_masking/core.html#IM_MSA_Transformer"><code>IM_MSA_Transformer</code></a>: Class with different functions used to generate new MSAs with the iterative masking procedure</p>
<p><a href="/Iterative_masking/core.html#gen_MSAs"><code>gen_MSAs</code></a>: example function (with parser) that can be used to generate and save new sequences directly from the terminal.</p>

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