Update as of 9.5.2018:
We are still working on improving the user experience with the Tigriopus genome. We have now fixed the links and presentation of the gene models in GBrowse. When clicking on a gene model, the links back to LiceBase should work correctly. We have also added Blast results against the L. salmonis predicted proteins and SwissProt to all predicted T. kingsejongensis genes.
When searching in Blast results, now it is possible to restrict the search to one organism. In addition, the maximal number of hits per query can be selected.
We are still working on:
- adding more Blast results (NR, selected arthropods)
- Other analyses (InterProScan, GO)
I have added the genome of the antarctic-endemic copepod Tigriopus kingsejongensis .
The genome and annotation data have been made publicly available in the GigaScience data archive, but so far no browsable genome exists. This version is slightly experimental
and not all the link-outs might work as perfectly as for L. salmonis yet. There is however:
- The genes and other features are available and searchable from within licebase: like this feature
- There is a GBrowse instance showing the sequence and gene-models, like this one
- Blast databases for the genome sequence and predicted proteins. Links from the Blast results back into LiceBase do not work properly yet. (should be fixed)
Because gene names in the T. king. annotation are not unique, the gene URLs in the whole data base had to be changed to enforce uniqueness constraints.
While links of the old format is like : https://licebase.org/?q=EMLSAG00000005383 (and still works), the new URL format is like so:
Most of you should not notice the new format however, unless you have stored links in external documents (Excel).
Kang S, Ahn DH, Lee JH, Lee SG, Shin SC, Lee J, Min GS, Lee H, Kim HW, Kim S,
Park H. The genome of the Antarctic-endemic copepod, Tigriopus kingsejongensis.
Gigascience. 2017 Jan 1;6(1):1-9. doi: 10.1093/gigascience/giw010. PubMed PMID:
28369352; PubMed Central PMCID: PMC5467011.