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jnavarr5
  Wed May 12 07:02:54 2021 -0700
Updating redirected links found the the uiLinks cronjob for danRer3, no Redmine

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 <h2>Description</h2>
 
 <p>
   This track shows <i>ab initio</i> predictions from the program
   <a href="http://bioinf.uni-greifswald.de/augustus/" target="_blank">AUGUSTUS</a> (version 3.1).
   The predictions are based on the genome sequence alone.
 </p>
 
 <p>
 For more information on the different gene tracks, see our <a target=_blank 
 href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>
 
 <h2>Methods</h2>
 
 <p>
 Statistical signal models were built for splice sites, branch-point
 patterns, translation start sites, and the poly-A signal.
 Furthermore, models were built for the sequence content of
 protein-coding and non-coding regions as well as for the length distributions
 of different exon and intron types. Detailed descriptions of most of these different models
 can be found in Mario Stanke's
-<a href="http://ediss.uni-goettingen.de/handle/11858/00-1735-0000-0006-B3F8-4" target="_blank">dissertation</a>.
+<a href="https://ediss.uni-goettingen.de/handle/11858/00-1735-0000-0006-B3F8-4" target="_blank">dissertation</a>.
 This track shows the most likely gene structure according to a
 Semi-Markov Conditional Random Field model.
 Alternative splicing transcripts were obtained with
 a sampling algorithm (<tt>--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2
 --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2</tt>).
 </p>
 
 <p>
 The different models used by Augustus were trained on a number of different species-specific
 gene sets, which included 1000-2000 training gene structures. The <tt>--species</tt> option allows
 one to choose the species used for training the models. Different training species were used
 for the <tt>--species</tt> option when generating these predictions for different groups of
 assemblies.
 <table class="stdTbl">
 	<tr>
 		<td align=center><b>Assembly Group</b></td>
 		<td align=center><b>Training Species</b></td>
 	</tr>
 	<tr>
 		<td align=center>Fish</td>
 		<td align=center><tt>zebrafish</tt>
 	</tr>
 	<tr>
 		<td align=center>Birds</td>
 		<td align=center><tt>chicken</tt>
 	</tr>
 	<tr>
 		<td align=center>Human and all other vertebrates</td>
 		<td align=center><tt>human</tt>
 	</tr>
 	<tr>
 		<td align=center>Nematodes</td>
 		<td align=center><tt>caenorhabditis</tt></td>
 	</tr>
 	<tr>
 		<td align=center>Drosophila</td>
 		<td align=center><tt>fly</tt></td>
 	</tr>
 	<tr>
 		<td align=center><em>A. mellifera</em></td>
 		<td align=center><tt>honeybee1</tt></td>
 	</tr>
 	<tr>
 		<td align=center><em>A. gambiae</em></td>
 		<td align=center><tt>culex</tt></td>
 	</tr>
 	<tr>
 		<td align=center><em>S. cerevisiae</em></td>
 		<td align=center><tt>saccharomyces</tt></td>
 	</tr>
 </table>
 <p>
 This table describes which training species was used for a particular group of assemblies.
 When available, the closest related training species was used.
 </p>
 
 <h2>Credits</h2>
 
 Thanks to the
 <a href="https://math-inf.uni-greifswald.de/en/department/about-us/employees/prof-dr-mario-stanke-english/"
 target="_blank">Stanke lab</a>
 for providing the AUGUSTUS program.  The training for the <tt>chicken</tt> version was
 done by Stefanie K&ouml;nig and the training for the
 <tt>human</tt> and <tt>zebrafish</tt> versions was done by Mario Stanke.
 
 <h2>References</h2>
 
 <p>
 Stanke M, Diekhans M, Baertsch R, Haussler D.
 <a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA"
 target="_blank">
 Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>.
 <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a>
 </p>
 
 <p>
 Stanke M, Waack S.
 <a href="https://academic.oup.com/bioinformatics/article/19/suppl_2/ii215/180603/Gene-prediction-with-a-hidden-Markov-model-and-a"
 target="_blank">
 Gene prediction with a hidden Markov model and a new intron submodel</a>.
 <em>Bioinformatics</em>. 2003 Oct;19 Suppl 2:ii215-25.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14534192" target="_blank">14534192</a>
 </p>