Administrator's blog

[Update] Blast searches under Feature - Homology

We have recently extended and update the pre-computed Blast analyses for all the gene features. From now on, we will run these analyses in a regular interval.

The following Blast analyses are available: 

To see the blast results, navigate to a gene feature (they are not available for transcripts or proteins at the moment, you have to go to the corresponding gene),

and click on the 'Homology' link to the left to open the Homology pane:

Homology

The following BLAST results are available for this feature:

Ensembl Metazoa release 31 - With Lepeophtheirus salmonis genome is public

Ensembl Metazoa release 31 - March 2016 has been published, and it contains the genome of the Atlantic salmon louse as a new species. All genes, transcripts and proteins in LiceBase will now be linked against their  Ensembl counterparts. The links appear under Cross references in each gene page.

RNAi form problems with IE [Fixed]

We have disabled the Overlay module for the the administrative interface because it was interfering with the RNAi edit interface.

The form validation did not work correctly, the tabs did not open automatically on error. This happened even with the latest version of Internet Explorer.

While we do not recommend IE for use by Administrators and Annotators, it should work for most of you now.

Maintenance downtime Monday, January 11 2016

There will be a scheduled maintenance downtime on Monday starting from 8 a.m. until approximately 3 p.m to perform necessary changes LiceBase and to finally migrate all user accounts to FEIDE.

During the downtime period, all LiceBase services including the genome browser and Blast will be unavailable or unstable. Please remember to log out from LiceBase by 6 am on January 11. We will send out a notification to all users once the the downtime is finshed, as always, this might take less time, but please don't rely on it.

Update: It is working again / Scheduled Downtime 4.-5. May

Update: the downtime is over LiceBase is working.

 

There will be a scheduled Downtime of LiceBase from Monday, 4.5.2015 10.00 am to Tuesday, 5..5.2015 12.00. We are going to do some mandatory maintanance tasks on our database servers. During this time you can experience instability, errors, or down-time of some or all the LiceBase services.

Even if the web-site is available in this period, we advise not to upload data or annotate experiments until we have announced that everything is cleared again.

We appologize for any inconvenience caused.    

 

[UPDATE] No option to extract spliced mRNA or CDS sequence from GBrowse or Tripal

It was noticed that it is not an easy task to extract the spliced mRNA sequence or CDS sequence directly from either GBrowse or Tripal. The annotated sequence of a Gene in Tripal will show the whole gene sequence, as well as the GBrowse CDS track: The CDS track details does not show only the coding sequence but the whole genomic sequence. 

It could be very useful to have an option to easily export only the coding part or only the mature mRNA sequence for designing primers. While it is possible to export a GFF file of the gene model plus the FASTA sequence of the whole chromosome and use an external genome viewer, I assume it might be a good idea to have this feature directly inside GBrowse or Tripal. We are aware of this requirement now and are looking into a solution. I have posted a more detailes question and solution on BioStars https://www.biostars.org/p/135429/

It seems that, until now, there hasn't been a good solution for this in GMOD. Now you can export spliced CDS from GBrowse. Export of the full mRNA, or UTR only, introns only, etc. is not yet implemented, but I am looking into it. 

Repeats track

Repetitive sequences are abundant in most eukaryote genomes. They pose difficulties for an exact reconstruction of the genomic sequence and also for primer design. They can also be useful as genetic markers, as micro- or mini-satelites.

Important: Please annotate phenotype CV

This is an important reminder for the annotation of RNAi experiments.

Please annotate the phenotype correctly after finishing the experiment. To fully annotate the phenotyp, please use the Phenotype CV field on the first page of the annotation, even if you have given a textual annotation of the phenotype. Please use No visible phenotype in case you do not see any phenotype. Please do not write "no phenotype" into the textual phenotype field because there might be an undetected phenotype anyway.

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