70952dc60bde84f731bfae4d9a7af4ba50b29bdb jnavarr5 Wed May 12 07:02:54 2021 -0700 Updating redirected links found the the uiLinks cronjob for danRer3, no Redmine diff --git src/hg/makeDb/trackDb/augustusGene.html src/hg/makeDb/trackDb/augustusGene.html index 619c816..e54872f 100644 --- src/hg/makeDb/trackDb/augustusGene.html +++ src/hg/makeDb/trackDb/augustusGene.html @@ -7,31 +7,31 @@ </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>