Bio-MUST-Apps-HmmCleaner
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<h1 class="title">User Guide for <code>HmmCleaner</code></h1>
<p class="author">
Arnaud Di Franco [<script type="text/javascript">
<!--
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</script><noscript>arnaud.difranco at sete dot cnrs dot fr</no...
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<p class="date">Version 0.1 / Feb 13, 2018</p>
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<div id="aim-and-features" class="titleslide slide section level1"><h1><span class="header-section-number">1</span> Aim and features</h1></div>
<div id="functional-overview" class="titleslide slide section level1"><h1><span class="header-section-number">2</span> Functional overview</h1></div><div id="profile-creation" class="slide section level2">
<h1><span class="header-section-number">2.1</span> Profile creation</h1>
<p><code>HmmCleaner</code> detects low similarity segments (LSS) through four steps. First, a pHMM is built from the MSA using <code>HMMER</code> (Figure 1A). This pHMM can be built upon either (i) all sequences of the MSA (complete strategy) or (ii)...
</div><div id="similarity-search" class="slide section level2">
<h1><span class="header-section-number">2.2</span> Similarity search</h1>
<p>Second, each sequence of the MSA is evaluated with the pHMM (Figure 1B), which yields profile-sequence alignments.</p>
</div><div id="score-analysis" class="slide section level2">
<h1><span class="header-section-number">2.3</span> Score analysis</h1>
<p>Third, the analysis of each profile-sequence alignment is based on the four discrete categories of column-wise probabilities provided by <code>HMMER</code>. The two first categories represent residues that fit poorly to the pHMM: blank character (...
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<div id="outputs" class="titleslide slide section level1"><h1><span class="header-section-number">3</span> Outputs</h1></div>
<div id="annexes" class="titleslide slide section level1"><h1><span class="header-section-number">4</span> Annexes</h1></div><div id="command-line-interface" class="slide section level2">
<h1><span class="header-section-number">4.1</span> Command line interface</h1>
<pre class="none"><code>USAGE
HmmCleaner.pl <infiles> [options]
REQUIRED ARGUMENTS
<infiles>
list of alignment file to check with HmmCleaner
OPTIONS
-costs <c1> <c2> <c3> <c4>
Cost parameters that defines the low similarity segments detected by
HmmCleaner. Default values are -0.15, -0.08, 0.15, 0.45 Users can
change each value but they have to be in increasing order. c1 < c2 <
0 < c3 < c4 Predefine value are also available with --large and
--specificity options but user defined costs will be prioritary if
present.
--changeID
Determine if output will have defline with generic suffix
(_hmmcleaned)
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