Genomicus v60.01

History of the browser & the database

2010-11-20.

Database (version 60.01)
- Update to Genomicus60.01 with the last Ensembl data (release 60)
- Additionnal species: Oikopleura dioica (Oikopleura) from Genoscope, Nematostella vectensis (Sea anemone) from JGI, Branchiostoma floridae (Amphioxus) from JGI
- New method of reconstruction of ancestral gene order (chromosome scale reconstruction is mostly achieved for mammals)
- Optimized database table structure to speed-up rendering
Webcode
- Collapsed nodes are now symbolized by a filled triangle
- Tree edition menu has been reworked (both views)
- On the first page, the user can choose "Default view" to go to a compact PhyloView, or "Custom view" to select AlignView or Phyloview, and the depth of analysis
- Various interface update
- Various bugfixes
- The website is fully compatible with HTML/XHTML/SVG/CSS standards, and thus with Firefox, Google Chrome and Safari

2010-09-15.

Database (version 59.01)
- Update to Genomicus59.01 with the last Ensembl data (release 59)
- Additionnal species: Oikopleura dioica (Oikopleura) from Genoscope, Nematostella vectensis (Sea anemone) from JGI, Branchiostoma floridae (Amphioxus) from JGI

2010-06-28.

Database (version 58.01)
- Update to Genomicus58.01 with the last Ensembl data (release 58)
- Additionnal species: Oikopleura dioica (Oikopleura) from Genoscope, Nematostella vectensis (Sea anemone) from JGI, Branchiostoma floridae (Amphioxus) from JGI

2010-03-15.

Database (version 57.01)
- Update to Genomicus57.01 with the last Ensembl data (release 57)
- Additionnal species: Oikopleura dioica (Oikopleura) from Genoscope, Nematostella vectensis (Sea anemone) from JGI, Branchiostoma floridae (Amphioxus) from JGI

2010-01-22.

Database (version 56.02)
- Complete genome annotation of Branchiostoma floridae, Oikopleura dioica and Nematostella vectensis. Before this, only the genes with at least one homolog in any other species were displayed
Webcode
- Nodes in the tree can now be hidden to make the display clearer
- In Phyloview, CNEs can be disabled
- Data from the current view can be exported in a text file
- The current display can be exported in a graphics file (SVG format). Users may then edit the figure and export it in PDF with softwares such as Inkscape
- A statistics page gives information on the data used and reconstructed in Genomicus

2009-11-20.

2009-10-20.

Database (version 56.01)
- CNEs are temporarely removed. All CNE positions for new assembly (Human version hg19, Bos taurus v4, zebrafish zv8) will be available very soon.

2009-10-07.

Database (version 56.01)
- Update to Genomicus56.01 with the last Ensembl data (release 56)
- Additionnal species: Oikopleura dioica (Oikopleura) from Genoscope, Nematostella vectensis (Sea anemone) from JGI, Branchiostoma floridae (Amphioxus) from JGI
- Ancestors' genes names are infered from Ensembl protein trees' names (ENSGT000xxxx). FAMxxxx are still used when genes of the above additonal species are involved.
Webcode
- Support of Internet Explorer via Google Chrome Frame

2009-07-21.

Database (version 55.01)
- Update to Genomicus55.01 with the last Ensembl data (release 55)
- Additionnal species: Oikopleura dioica (Oikopleura) from Genoscope, Nematostella vectensis (Sea anemone) from JGI, Branchiostoma floridae (Amphioxus) from JGI
Webcode
- Successive versions of Genomicus are now archived and available online. The new URL scheme is www.dyogen.ens.fr/genomicus for the most recent database and www.dyogen.ens.fr/genomicus-XX.XX for specific versions (permanent links)

2009-06-14.

Database (version 54.01)
- Update to Genomicus54.01 with the last Ensembl data (release 54)
- additionnal species: Oikopleura dioica (Oikopleura) from Genoscope, Nematostella vectensis (Nematostella) from JGI, Branchiostoma floridae (Amphioxus) from JGI

2009-04-03.

Webcode
- In «AlignView», some situations with non-conserved gene neighbouring were represented with thicks lines instead of white space
- Various optimisations that should improve server response

2009-03-20.

2009-03-17.

Webcode
- The colour/symbol code is now consistent with Ensembl & TreeFam
- The link to Ensembl GeneView is now working
- Our mail adress has changed and now works

2009-03-12.

Webcode
- A «alignment view» is now available, and the previous mode of display is now «Phyloview». A button allows to switch between both views without starting a new search
- A two-state button 'Reference order'/'Adaptative order' changes the order of modern species to highlight the genome evolution from the root species to the current reference species
Database (version 53.01)
- Synteny blocks have been updated with the last Ensembl data (release 53). Thanks to the addition of new key amniote genomes such as zebra finch or lizard, synteny blocks are much longer at Amniota & Mammalia nodes

2008-11-01.

Webcode
- The menu to select extant and ancestral species has been tidyed up
- A history page has been added
- Some links to customize the tree view have been added
- The search engine now displays a message when the query gene has no orthologues
Database (version 50.02)
- A bug in the display of amphioxus genes has been corrected: most genes were previously shown below an artefactual duplication node, which have now been removed. This does not affect the number of amphioxus genes displayed nor their phylogenic relationship with other species
- Now only duplication nodes with a confidence index (as provided by Ensembl) of 0.3 or more are taken into account. Duplication nodes below this value are propagated to terminal branches and thus turned into species specific duplications. The consequence is the removal of several thousand ancestral genes per ancestral species which were likely artefactual. Syntenic blocks are now longer and more reliable

2008-10-01.

Version scheme.

The web-code is referred with the date of its release
The database version is composed of two numbers:
- The version of the Ensembl database used to define the gene annotations and the protein trees
- The version of the reconstructions (synteny, ancestral gene order & conserved non-coding elements)