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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
<html><head><title></title>
<link rel="stylesheet" type="text/css" href="augustus.css">
<script src="tutorial.js" type="text/javascript"></script>
</head><body>
<font size=-1>
Navigate to
<a href="scipio.html">Using Scipio</a>.
<a href="training.html">Training AUGUSTUS</a>.
<a href="prediction.html">Predicting Genes</a>.
<a href="ppx.html">AUGUSTUS-PPX</a>.
</font>
<h1>Lab Session on Gene Prediction with <a href="http://bioinf.uni-greifswald.de/augustus/">AUGUSTUS</a></h1>
<h2><a href="http://www.molecularevolution.org">Workshop on Comparative Genomics</a>, Jan. 14th 2011, <a href="http://www.math-inf.uni-greifswald.de/mathe/index.php/mitarbeiter/382-prof-dr-mario-stanke">Mario Stanke</a></h2>
In this lab session we practice the most common Bioinformatics steps when predicting the protein-coding genes in
a eukaryotic genome with <a href="http://bioinf.uni-greifswald.de/augustus/">AUGUSTUS</a>. We will assume the case of a "new"
genome, for which AUGUSTUS has not been trained before, but will use well-studied species as examples because
example data is readily available and visualization is easier.
<h4>Styles</h4>
<p><span class="assignment">Assignments are in this color</span>. The lazy ones may go through very
fast through this tutorial by just reading these assignments and cutting and pasting the commands
that follow them (more or less).</p>
<p>
<span class="result">Results are in this color</span>.<br></p>
<p>
<a href="javascript:onoff('explain')" class="dlink"><span id="explain" title="explaind" class="dcross">[+]</span>
<span class="dtitle">Details are hidden...</span></a> <br>
<div id="explaind" class="details" style="display:none;">
You don't have to read this. If you get bored with the speed of the tutorial then you can read these details boxes.
</div></p>
<h3>Example Data</h3>
All example files are in the <a href="data/" target="_blank">data directory</a>. We recommend
you work directly in this directory.
<h4><i>Drosophila melanogaster</i> (Exercises 1-5)</h4>
<ul>
<li> <a href="data/chr2R.fa"><tt>chr2R.fa</tt></a>: chromosome 2R of assembly dm3 of the genome of the fruit fly</li>
<li><a href="data/chr2R.2M-7M.fa"><tt>chr2R.2M-7M.fa</tt></a>: 5 megabases 2,000,001-7,000,000
of chromosome 2R.<br>
</li>
<li><a href="data/chr2R.2M-7M.aa"><tt>chr2R.2M-7M.aa</tt></a>: amino acid sequences of 1117 flybase genes from the same 5Mb</li>
<li><a href="data/est.chr2R.7M-8M.fa"><tt>est.chr2R.7M-8M.fa</tt></a>: a set of 8458 ESTs
which map to chr2R:7000000-8000000
</li>
<li><a href="data/chr2R.7M-8M.wig"><tt>chr2R.7M-8M.wig</tt></a>: coverage from RNA-Seq in chr2R:7000000-8000000</li>
<li><a href="data/hints.rnaseq.intron.gff"><tt>hints.rnaseq.intron.gff</tt></a>: likely intron positions inferred from RNA-Seq alignments</li>
</ul>
<h4>Human (Exercises 6)</h4>
<ul>
<li> <a href="data/chr3.42M.fa"><tt>chr3.42M.fa</tt></a>, <a href="data/chr5.124M.fa"><tt>chr5.124M.fa</tt></a>, <a href="data/chr4.103M.fa"><tt>chr4.103M.fa</tt></a>: 2 mega bases each of the human genome (hg19)</li>
<li>
<a href="data/PF00225_seed.txt"><tt>PF00225_seed.txt</tt></a>,
<a href="data/PF00225_full.txt"><tt>PF00225_full.txt</tt></a>,
<a href="data/PF00171_seed.txt"><tt>PF00171_seed.txt</tt></a>,
<a href="data/PF00171_full.txt"><tt>PF00171_full.txt</tt></a>: multiple sequence alignments
of two protein families in FASTA format</li>
</ul>
<h3>For Cheaters: <span class="result">Result Files</span></h3>
You can use the <a href="results/" target="_blank">files in the results directory</a> to catch on if you are behind or to compare your results.
<br>
<h3>Exercise 1: <span class="assignment">Compile a Training Set</span></h3>
There are several typical <a href="training.html#trainoptions">options for creating a training set</a>
to estimate the parameters of gene finders. We will here go through option 4:
<p style="margin-left:50px">
<i>Spliced alignments of protein sequences</i>
</p>
We assume that we have a set of protein sequences of the same or a very closely related species and will use <a href="http://www.webscipio.org/">Scipio</a> to infer the gene structures.<br>
<ol>
<li><span class="assignment">Follow the tutorial on <a href="scipio.html">"Using Scipio to create a training set"</a></span>
and create a training set <tt>genes.gb</tt>.
<li><span class="assignment">Partition <tt>genes.gb</tt></span> into a training set and a holdout test setas described in <a href="training.html#split">1.2 Split gene structure set...</a>.
</ol>
<h3>Exercise 2: <span class="assignment">Train the Coding Regions of AUGUSTUS</span></h3>
Let's name our species "<tt>bug</tt>". Pretending that there was not already a parameters set of AUGUSTUS for
<i>Drosophila</i> (named "<tt>fly</tt>"), we will estimate the parameters from the training set.
<ol>
<li> <span class="assignment">Create a meta parameters file</span> for <tt>bug</tt> as described in <a href="training.html#meta">2. CREATE A META PARAMETERS FILE...</a>
<li> <span class="assignment">Estimate the parameters</span> using your training set as described in <a href="training.html#etraining">3. MAKE AN INITIAL TRAINING</a>
</ol>
<h3>Exercise 3: <span class="assignment"><i>Ab Initio</i> Predict Genes in the Genome</span></h3>
<ol>
<li> <span class="assignment">Predict the protein-coding parts of the genes</span>
in a sample sequence of <i>Drosophila melanogaster</i> as described in
<a href="prediction.html#abinitiopred">1. PREDICT GENES AB INITIO</a>.
<li> <span class="assignment">Visualize your predicted genes</span> as decribed in <a href="prediction.html#customtrack">2. MAKE A CUSTOM GENE PREDICTION TRACK...</a>.
</ol>
<h3>Exercise 4: <span class="assignment">Prepare hints</span></h3>
Construct extrinsic evidence about genes from transcriptome data (ESTs and RNA-Seq) following
the intructions in <a href="prediction.html#prephints">3. PREPARE HINTS</a>.
<h3>Exercise 5: <span class="assignment">Predict Genes Using Hints</span></h3>
Structurally annotate an example sequence from Drosophila based on the hints from exercise 4 by
<ol>
<li><span class="assignment"><a href="prediction.html#extr">setting the hint parameters</a></span>
<li><span class="assignment"><a href="prediction.html#predh">predicting genes using hints</a></span>
</ol>
<h3>Exercise 6: <span class="assignment">Identify Members of a Protein Family</span></h3>
Use the new PPX-Extension of AUGUSTUS to find the gene structures
based on a multiple alignment of a protein family as described in
<a href="ppx.html">AUGUSTUS-PPX</a>.
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