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<body>
<div class="document" id="last-train">
<h1 class="title">last-train</h1>
<p>last-train finds the rates (probabilities) of insertion, deletion, and
substitutions between two sets of sequences. It thereby finds
suitable substitution and gap scores for aligning them.</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 <a class="reference external" href="lastal.html#score-options">lastal's -p
option</a>.</p>
<p>last-train can read .gz files, or from pipes:</p>
<pre class="literal-block">
bzcat queries.fasta.bz2 | last-train mydb
</pre>
<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>
<tr><td class="option-group">
<kbd><span class="option">-v</span>, <span class="option">--verbose</span></kbd></td>
<td>Show more details of intermediate steps.</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 "special".</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 > PID% identity. This aims to
optimize the parameters for low-similarity alignments
(similarly to the BLOSUM matrices).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--postmask=<var>NUMBER</var></span></kbd></td>
<td>By default, last-train ignores alignments of mostly-lowercase
sequence (by using <a class="reference external" href="last-postmask.html">last-postmask</a>).
To turn this off, do <tt class="docutils literal"><span class="pre">--postmask=0</span></tt>.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--sample-number=<var>N</var></span></kbd></td>
<td>Use N randomly-chosen chunks of the query sequences. The
queries are chopped into fixed-length chunks (as if they were
first concatenated into one long sequence). If there are ≤ N
chunks, all are picked. Otherwise, if the final chunk is
shorter, it is never picked. 0 means use everything.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--sample-length=<var>L</var></span></kbd></td>
<td>Use randomly-chosen chunks of length L.</td></tr>
</tbody>
</table>
</blockquote>
<p>All options below this point are passed to lastal to do the
alignments: they are described in more detail at <a class="reference external" href="lastal.html">lastal.html</a>.</p>
</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. (See <a class="reference external" href="last-evalues.html">here</a>.)</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. (See <a class="reference external" href="last-evalues.html">here</a>.)</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><p class="first">Specify how to use the substitution score matrix for
reverse strands. If you use <tt class="docutils literal"><span class="pre">--revsym</span></tt>, this makes no
difference. "0" means that the matrix is used as-is for
all alignments. "1" (the default) means that the matrix
is used as-is for alignments of query sequence forward
strands, and the complemented matrix is used for query
sequence reverse strands.</p>
<p class="last">This parameter is always written in last-train's output,
so it will override lastal's default.</p>
</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-C <var>COUNT</var></span></kbd></td>
<td>Before extending gapped alignments, discard any gapless
alignment whose query range lies in COUNT other gapless
alignments with higher score-per-length. This aims to
reduce run time.</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">-k <var>STEP</var></span></kbd></td>
<td>Look for initial matches starting only at every STEP-th
position in each query.</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><p class="first">How to read the query sequences. By default, they must
be in <tt class="docutils literal">fasta</tt> format. <tt class="docutils literal"><span class="pre">-Q0</span></tt> means <tt class="docutils literal">fasta</tt> or
<tt class="docutils literal"><span class="pre">fastq-ignore</span></tt>. <tt class="docutils literal"><span class="pre">-Q1</span></tt> means <tt class="docutils literal"><span class="pre">fastq-sanger</span></tt>.</p>
<p>The <tt class="docutils literal">fastq</tt> formats are described here:
<a class="reference external" href="lastal.html">lastal.html</a>. <tt class="docutils literal"><span class="pre">fastq-ignore</span></tt> means that the
quality data is ignored, so the results will be the same
as for <tt class="docutils literal">fasta</tt>.</p>
<p>For <tt class="docutils literal"><span class="pre">fastq-sanger</span></tt>, last-train assumes the quality
codes indicate substitution error probabilities, <em>not</em>
insertion or deletion error probabilities. If this
assumption is dubious (e.g. for data with many insertion
or deletion errors), it may be better to use
<tt class="docutils literal"><span class="pre">fastq-ignore</span></tt>. For <tt class="docutils literal"><span class="pre">fastq-sanger</span></tt>, last-train finds
the rates of substitutions not explained by the quality
data (ideally, real substitutions as opposed to errors).</p>
<p class="last">If specified, this parameter is written in last-train's
output, so it will override lastal's default.</p>
</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. If it fails to find any alignments, you could try
<a class="reference external" href="last-tutorial.html#example-6-find-very-short-dna-alignments">reducing the alignment significance threshold</a> with
option -D.</p>
</li>
<li><p class="first">last-train cannot handle DNA-versus-protein alignment.</p>
</li>
</ul>
</div>
</div>
</body>
</html>
|
