Answers.Body: <p>The UCSC genome browser supports local mirrors. You could make a local mirror that has the "TransMap Alignments" cross-species gene track. From the <a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=660022369_AUzllaH1GkM6HAQrM1t7y25Cdpme&amp;c=chr5&amp;g=transMapV4" rel="nofollow noreferrer">track description page</a>:</p>
  
  <blockquote>
    <p>These tracks contain cDNA and gene alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered LASTZ or BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human. For more distant organisms, reciprocal best alignments are used.</p>
  </blockquote>
  
  <p>They provide a helpful tutorial on setting up a local installation <a href="https://genome.ucsc.edu/goldenpath/help/mirror.html" rel="nofollow noreferrer">here</a>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-03-13T16:59:13.567Z
Answers.LastActivityDate: 2018-03-13T16:59:13.567Z
Answers.UserDisplayName: Ben D.
Answers.Body: <p>Have a look at <a href="https://www.ibens.bio.ens.psl.eu/spip.php?article175&amp;lang=fr" rel="nofollow noreferrer">Genomicus</a></p>
  <p>Example for a <em>A. thaliana</em> gene across plants: <a href="https://www.genomicus.bio.ens.psl.eu/genomicus-plants-49.01/cgi-bin/phyloview.pl?root=1681867&amp;id=1681940" rel="nofollow noreferrer">https://www.genomicus.bio.ens.psl.eu/genomicus-plants-49.01/cgi-bin/phyloview.pl?root=1681867&amp;id=1681940</a></p>
  <p>I'm not sure that you can install it locally, though.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-08-28T15:17:32.903Z
Answers.LastActivityDate: 2024-08-28T15:17:32.903Z
Answers.UserDisplayName: bricoletc
Body: <p>I found that there is a Syntenic gene browser at <a href="https://genomevolution.org/wiki/index.php/Syntenic_gene_sets" rel="nofollow noreferrer">GEvo</a>. Do anyone know where could I find a similar browser for a local installation?</p>
  
Tags: <sequence-annotation><genome-browser>
Title: Syntenic gene browser
ThreadText: # Syntenic gene browser
  
  (Asked by: username_0 on 2018-03-09)
  
  I found that there is a Syntenic gene browser at [GEvo](https://genomevolution.org/wiki/index.php/Syntenic_gene_sets). Do anyone know where could I find a similar browser for a local installation?
  
  **Tags:** sequence-annotation, genome-browser
  
  
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  ## 2 answers
  
  ### Answer by username_1 on 2018-03-13. Score: 1
  
  The UCSC genome browser supports local mirrors. You could make a local mirror that has the "TransMap Alignments" cross-species gene track. From the [track description page](https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=660022369_AUzllaH1GkM6HAQrM1t7y25Cdpme&c=chr5&g=transMapV4):
  
  > These tracks contain cDNA and gene alignments produced by the TransMap cross-species alignment algorithm from other vertebrate species in the UCSC Genome Browser. For closer evolutionary distances, the alignments are created using syntenically filtered LASTZ or BLASTZ alignment chains, resulting in a prediction of the orthologous genes in human. For more distant organisms, reciprocal best alignments are used.
  
  They provide a helpful tutorial on setting up a local installation [here](https://genome.ucsc.edu/goldenpath/help/mirror.html).
  
  
  ---
  
  ### Answer by username_2 on 2024-08-28. Score: 0
  
  Have a look at [Genomicus](https://www.ibens.bio.ens.psl.eu/spip.php?article175&lang=fr)
  
  Example for a *A. thaliana* gene across plants: <https://www.genomicus.bio.ens.psl.eu/genomicus-plants-49.01/cgi-bin/phyloview.pl?root=1681867&id=1681940>
  
  I'm not sure that you can install it locally, though.
  
  
  ---
  
  