Michael Dondrup's blog

Update: Tigriopus kingsejongensis Genome

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.

Core Update Completed

Dear LiceBase users,

after a long update process, LiceBase is finally back up. You may now log in again, and you will find that no data was lost in the update process. Please report any problem you are experiencing to us. The differences between the new and previous versions with respect to the user interface will be appear as mostly minor.

The largest differences are:

Problems after Feide migration? (Read this)

LiceBase.org is now officially a Feide registered service provider. Users from the academic partners UiB and NMBU are able to log in using their organizatioal accounts.

So far, we haven't heard of any problems after the Feide migration, and are seeing that people seem to be happily using the migrated user profiles. So overall this was a big success :D

New Control Sequences CPY185 CTH210 CMi2471

CPY185 is the common negative control sequence for RNAi experiments. I have uploaded the sequence for use in the RNAi experiment annotation: https://licebase.org/CPY185%20%28negative%20control%29

Two more control candidates have been added:

Both are PCR products from transcribed mRNA in the Atlantic Cod.

NeLS Workshop

Sitting in the NeLS workshop at CBU right now:

  • NeLS starting page (NeLS = Norwegian e-Infrastructure for LifeScience research)
  • NeLS is funded by Elixir.no
  • You can log in with your FEIDE (University account)
  • NeLS storage is NeLS's cloud storage solution


Caligus rogercresseyi transcriptome BLAST database

TSA: Caligus rogercresseyi, transcriptome shotgun assembly

GenBank: GAZX00000000.1

is provided as a BLAST database. If you want to blast against the closest related transcriptome available as of today, visit the BLAST page and select the Caligus rogercresseyi transcriptome database. This is a nucleotide database, most useful probably with a translated BLAST program, either TBLASTN (protein input vs. translated db), or TBLASTX (translated nucleotide query vs translated db).

[Update] Blast vs. Genome shows overlapping features

I have updated the Blast server slightly, following Heidi's request:
When using BlastN or TBlastX vs. genomic scaffolds (LSalAtl2s masked and unmasked, but not "Everything L. Salmonis) the result page will list all genomic features that overlap with the location of the hit. This is very handy to test e.g. if primers or other short sequences hit the correct gene.

Details: this has not been implemented by making a new database with the gene sequences only. Instead the overlaps are computed from the annotation on the fly. This has several advantages:

Feature: Help, my favorite gene is missing in the genome!

"Help, the gene I am working with is not present in the genome!"

Users start noticing that some of the genes they are working with cannot be found in the current genome annotation, and they start complaining about it. This is in fact a good approach, because only when problems are reported can we notice them and possibly work on a fix. It is less favorable though that the natural shortcomings of our genome assembly could be also reflected onto the database containing it (e.g. LiceBase), even though the database system and the genome sequence it represents are two related but distinct artifacts (or pieces of "software").


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