/usr/share/doc/last-align/last-train.html

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<body>
<div class="document" id="last-train">
<h1 class="title">last-train</h1>

<p>This script tries to find suitable score parameters (substitution and
gap scores) for aligning some given sequences.</p>
<p>It (probabilistically) aligns the sequences using some initial score
parameters, then estimates better score parameters based on the
alignments, and repeats this procedure until the parameters stop
changing.</p>
<p>The usage is like this:</p>
<pre class="literal-block">
lastdb mydb reference.fasta
last-train mydb queries.fasta
</pre>
<p>last-train prints a summary of each alignment step, followed by the
final score parameters in a format that can be read by lastal's -p
option.</p>
<div class="section" id="options">
<h2>Options</h2>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">-h</span>, <span class="option">--help</span></kbd></td>
<td>Show a help message, with default option values, and exit.</td></tr>
</tbody>
</table>
</blockquote>
<div class="section" id="training-options">
<h3>Training options</h3>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">--revsym</span></kbd></td>
<td>Force the substitution scores to have reverse-complement
symmetry, e.g. score(A→G) = score(T→C).  This is often
appropriate, if neither strand is &quot;special&quot;.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--matsym</span></kbd></td>
<td>Force the substitution scores to have directional symmetry,
e.g. score(A→G) = score(G→A).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--gapsym</span></kbd></td>
<td>Force the insertion costs to equal the deletion costs.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--pid=<var>PID</var></span></kbd></td>
<td>Ignore alignments with &gt; PID% identity.  This aims to
optimize the parameters for low-similarity alignments,
similarly to the BLOSUM matrices.</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="initial-parameter-options">
<h3>Initial parameter options</h3>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">-r <var>SCORE</var></span></kbd></td>
<td>Initial match score.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-q <var>COST</var></span></kbd></td>
<td>Initial mismatch cost.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-p <var>NAME</var></span></kbd></td>
<td>Initial match/mismatch score matrix.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-a <var>COST</var></span></kbd></td>
<td>Initial gap existence cost.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-b <var>COST</var></span></kbd></td>
<td>Initial gap extension cost.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-A <var>COST</var></span></kbd></td>
<td>Initial insertion existence cost.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-B <var>COST</var></span></kbd></td>
<td>Initial insertion extension cost.</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="alignment-options">
<h3>Alignment options</h3>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">-D <var>LENGTH</var></span></kbd></td>
<td>Query letters per random alignment.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-E <var>EG2</var></span></kbd></td>
<td>Maximum expected alignments per square giga.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-s <var>NUMBER</var></span></kbd></td>
<td>Which query strand to use: 0=reverse, 1=forward, 2=both.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-S <var>NUMBER</var></span></kbd></td>
<td>Score matrix applies to forward strand of: 0=reference,
1=query.  This matters only if the scores lack
reverse-complement symmetry.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-T <var>NUMBER</var></span></kbd></td>
<td>Type of alignment: 0=local, 1=overlap.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-m <var>COUNT</var></span></kbd></td>
<td>Maximum number of initial matches per query position.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-P <var>COUNT</var></span></kbd></td>
<td>Number of parallel threads.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-Q <var>NUMBER</var></span></kbd></td>
<td>Query sequence format: 0=fasta, 1=fastq-sanger.
<strong>Important:</strong> if you use option -Q, last-train will only
train the gap scores, and leave the substitution scores
at their initial values.</td></tr>
</tbody>
</table>
</blockquote>
</div>
</div>
<div class="section" id="bugs">
<h2>Bugs</h2>
<ul>
<li><p class="first">last-train assumes that gap lengths roughly follow a geometric
distribution.  If they do not (which is often the case), the results
may be poor.</p>
</li>
<li><p class="first">last-train can fail for various reasons, e.g. if the sequences are
too dissimilar.</p>
</li>
</ul>
</div>
</div>
</body>
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last-align 712-1ubuntu1 / usr / share / doc / last-align / last-train.html
