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ComparaAPI.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title id="doctitle">Compara API Exercises</title>
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<h1>This workshop</h1>
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<h2>GenomeDB</h2>
<p>A GenomeDB is used to link the Compara database to each of the Core species databases.</p>
<h3>1. <u>Print the name, assembly version and genebuild version for all the GenomeDBs in the compara DB</u></h3>
<ul>
<li>Solution: [<a href="solutions/genome_db1.pl.html">html</a>/<a href="solutions/genome_db1.pl">text</a>] [<a href="solutions/genome_db1.txt">output</a>]</li>
</ul>
<p></p>
<h2>DnaFrag</h2>
<p>A DnaFrag represents a top-level SeqRegion in the Compara database</p>
<h3>1. <u>Print all the DnaFrags for chimp</u></h3>
<ul>
<li>Solution 1: [<a href="solutions/dnafrag1.pl.html">html</a>/<a href="solutions/dnafrag1.pl">text</a>] [<a href="solutions/dnafrag1.txt">output</a>]</li>
</ul>
<p></p>
<h2>MethodLinkSpeciesSet</h2>
<p>The MethodLinkSpeciesSet is a central component in the Compara database, it stores information connecting the various analyses (method) with a set of species (species_set_obj)</p>
<h3>1. <u>Print the total number of MethodLinkSpeciesSet entries stored in the database</u></h3>
<h3>2. <u>Print a unique list of method_link_types and a count of their number in the database</u></h3>
<h3>3. <u>Print a list of the species and their internal Ids (dbIDs) for the 12 eutherian mammal EPO alignments</u></h3>
<ul>
<li>Solution 1: [<a href="solutions/method_link_species_set1.pl.html">html</a>/<a href="solutions/method_link_species_set1.pl">text</a>] [<a href="solutions/method_link_species_set1.txt">output</a>]</li>
<li>Solution 2: [<a href="solutions/method_link_species_set2.pl.html">html</a>/<a href="solutions/method_link_species_set2.pl">text</a>] [<a href="solutions/method_link_species_set2.txt">output</a>]</li>
<li>Solution 3: [<a href="solutions/method_link_species_set3.pl.html">html</a>/<a href="solutions/method_link_species_set3.pl">text</a>] [<a href="solutions/method_link_species_set3.txt">output</a>]</li>
</ul>
<p></p>
<h2>GenomicAlignBlock</h2>
<p>A GenomicAlignBlock represents an alignment between two or more pieces of DNA. Every piece of DNA is represented by a GenomicAlign</p>
<h3>1. <u>Print the LASTZ_NET alignments for pig chromosome 15 with cow (using pig coordinates 89151597 and 89157190)</u></h3>
<h3>2. <u>Change the above example so that it prints the alignments for the 12 eutherian mammals EPO</u></h3>
<ul>
<li>Solution 1:
<ul>
<li>option a: [<a href="solutions/genomic_align_block1a.pl.html">html</a>/<a href="solutions/genomic_align_block1a.pl">text</a>] [<a href="solutions/genomic_align_block1a.txt">output</a>]</li>
<li>option b: [<a href="solutions/genomic_align_block1b.pl.html">html</a>/<a href="solutions/genomic_align_block1b.pl">text</a>] [<a href="solutions/genomic_align_block1b.txt">output</a>]</li>
</ul></li>
<li>Solution 2: [<a href="solutions/genomic_align_block2.pl.html">html</a>/<a href="solutions/genomic_align_block2.pl">text</a>] [<a href="solutions/genomic_align_block2.txt">output</a>]</li>
</ul>
<p></p>
<h2>ConstrainedElements</h2>
<p>A Constrained Element represents regions in the multiple alignment which appear to be under evolutionary constraint.</p>
<h3>1. <u>Print the constrained element alignments from the previous pig locus (use theConstrained elements generated from the EPO_LOW_COVERGAGE mammals alignments)</u></h3>
<ul>
<li>Solution 1: [<a href="solutions/constrained_element1.pl.html">html</a>/<a href="solutions/constrained_element1.pl">text</a>] [<a href="solutions/constrained_element1.txt">output</a>]</li>
</ul>
<p></p>
<h2>Synteny</h2>
<p></p>
<h3>1. <u>Print the pig-cow syntenic map for the pig chr. 15</u></h3>
<ul>
<li>Solution 1: [<a href="solutions/synteny1.pl.html">html</a>/<a href="solutions/synteny1.pl">text</a>] [<a href="solutions/synteny1.txt">output</a>]</li>
</ul>
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