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mm39.trackDb.html : Differences exist between hgwbeta and hgw2 

(RR fields taken from public MySql server, not individual machine)

1755,1838d1754
< HLTOGAannotvHg38v1 | html
< HLTOGAannotvHg38v1 | <h2>Description</h2>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | <b>TOGA</b>
< HLTOGAannotvHg38v1 | (<b>T</b>ool to infer <b>O</b>rthologs from <b>G</b>enome <b>A</b>lignments)
< HLTOGAannotvHg38v1 | is a homology-based method that integrates gene annotation, inferring
< HLTOGAannotvHg38v1 | orthologs and classifying genes as intact or lost.
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | 
< HLTOGAannotvHg38v1 | <h2>Methods</h2>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | As input, <b>TOGA</b> uses a gene annotation of a reference species
< HLTOGAannotvHg38v1 | (human/hg38 for mammals, chicken/galGal6 for birds) and
< HLTOGAannotvHg38v1 | a whole genome alignment between the reference and query genome.
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | <b>TOGA</b> implements a novel paradigm that relies on alignments of intronic
< HLTOGAannotvHg38v1 | and intergenic regions and uses machine learning to accurately distinguish
< HLTOGAannotvHg38v1 | orthologs from paralogs or processed pseudogenes.
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | To annotate genes,
< HLTOGAannotvHg38v1 | <a href="https://academic.oup.com/bioinformatics/article/33/24/3985/4095639"
< HLTOGAannotvHg38v1 | target="blank">CESAR 2.0</a>
< HLTOGAannotvHg38v1 | is used to determine the positions and boundaries of coding exons of a
< HLTOGAannotvHg38v1 | reference transcript in the orthologous genomic locus in the query species.
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | 
< HLTOGAannotvHg38v1 | <h2>Display Conventions and Configuration</h2>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | Each annotated transcript is shown in a color-coded classification as
< HLTOGAannotvHg38v1 | <ul>
< HLTOGAannotvHg38v1 | <li><span style='display:inline-block; width:40px; height:15px; background-color:blue;'>&nbsp;</span>
< HLTOGAannotvHg38v1 |     <span style='color:blue'>"intact"</span>: middle 80% of the CDS
< HLTOGAannotvHg38v1 |     (coding sequence) is present and exhibits no gene-inactivating mutation.
< HLTOGAannotvHg38v1 |     These transcripts likely encode functional proteins.</li>
< HLTOGAannotvHg38v1 | <li><span style='display:inline-block; width:40px; height:15px; background-color:lightblue;'>&nbsp;</span>
< HLTOGAannotvHg38v1 |     <span style='color:#7193a0'>"partially intact"</span>: 50% of the CDS
< HLTOGAannotvHg38v1 |      is present in the query and the middle 80% of the CDS exhibits no
< HLTOGAannotvHg38v1 |      inactivating mutation. These transcripts may also encode functional
< HLTOGAannotvHg38v1 |      proteins, but the evidence is weaker as parts of the CDS are missing,
< HLTOGAannotvHg38v1 |      often due to assembly gaps.</li>
< HLTOGAannotvHg38v1 | <li><span style='display:inline-block; width:40px; height:15px; background-color:grey;'>&nbsp;</span>
< HLTOGAannotvHg38v1 |     <span style='color:grey'>"missing"</span>: &lt;50% of the CDS is present
< HLTOGAannotvHg38v1 |      in the query and the middle 80% of the CDS exhibits no inactivating
< HLTOGAannotvHg38v1 |      mutation.</li>
< HLTOGAannotvHg38v1 | <li><span style='display:inline-block; width:40px; height:15px; background-color:orange;'>&nbsp;</span>
< HLTOGAannotvHg38v1 |     <span style='color:orange'>"uncertain loss"</span>: there is 1
< HLTOGAannotvHg38v1 |      inactivating mutation in the middle 80% of the CDS, but evidence is not
< HLTOGAannotvHg38v1 |      strong enough to classify the transcript as lost. These transcripts may
< HLTOGAannotvHg38v1 |      or may not encode a functional protein.</li>
< HLTOGAannotvHg38v1 | <li><span style='display:inline-block; width:40px; height:15px; background-color:red;'>&nbsp;</span>
< HLTOGAannotvHg38v1 |     <span style='color:red'>"lost"</span>: typically several inactivating
< HLTOGAannotvHg38v1 |      mutations are present, thus there is strong evidence that the transcript
< HLTOGAannotvHg38v1 |      is unlikely to encode a functional protein.</li>
< HLTOGAannotvHg38v1 | </ul>
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | Clicking on a transcript provides additional information about the orthology
< HLTOGAannotvHg38v1 | classification, inactivating mutations, the protein sequence and protein/exon
< HLTOGAannotvHg38v1 | alignments.
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | 
< HLTOGAannotvHg38v1 | <h2>Credits</h2>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | This data was prepared by the <a href="https://tbg.senckenberg.de/hillerlab/"
< HLTOGAannotvHg38v1 | target="_blank">Michael Hiller Lab</a>
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | 
< HLTOGAannotvHg38v1 | <h2>References</h2>
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | The <b>TOGA</b> software is available from
< HLTOGAannotvHg38v1 | <a href="https://github.com/hillerlab/TOGA"
< HLTOGAannotvHg38v1 | target="_blank">github.com/hillerlab/TOGA</a>
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 | 
< HLTOGAannotvHg38v1 | <p>
< HLTOGAannotvHg38v1 | Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales A,
< HLTOGAannotvHg38v1 | Ahmed AW, Kontopoulos DG, Hilgers L, Zoonomia Consortium, Hiller M.
< HLTOGAannotvHg38v1 | <a href="https://www.biorxiv.org/content/10.1101/2022.09.08.507143v1"
< HLTOGAannotvHg38v1 | target="_blank">TOGA integrates gene annotation with orthology inference
< HLTOGAannotvHg38v1 | at scale</a>. <em>bioRxiv preprint September 2022</em>
< HLTOGAannotvHg38v1 | </p>
< HLTOGAannotvHg38v1 |