[News] InterProScan results uploaded

Submitted by Administrator on 6 May, 2014 - 18:37

Results from a run of InterProScan5 have been uploaded to LiceBase. InterProScan was run on the protein sequences for all predicted Ensembl proteins in L.salmonis. InterProScan reports are linked to Proteins, to access them, search for the protein of interest (e.g. EMLSAP0000002400) using

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Blast vs. GO annotation added

Submitted by Administrator on 3 April, 2014 - 11:32

I have imported a Blastp run vs. all Gene Ontology sequences to extract GO terms annotations. The results of these run are available for features of type Gene.

They appear as a link called GO homologs on the right side in the Resources menu see e.g.: https://licebase.org/EMLSAG00000009076-691842#tripal_analysis_blast-results-61-box

[News] RNA-seq FPKM track updated

Submitted by Michael Dondrup on 24 March, 2014 - 12:30

I have update the FPKM data track in GBrowse with the new FPKM data. To enable the view of expression profiles for all new and old data sets:

[NEWS] Strand specific RNA-seq tracks added

Submitted by Administrator on 19 March, 2014 - 16:12

We have added strand specific RNA-seq coverage tracks to GBrowse, you can enable them under "Select tracks"->"Reads".

A transparently overlapping plot is depicted for each experiment. You can enable or disable strands under "Showing 1/2 subtracks", by default only forward strand is on.

[NEWS] LiceBase Officially in Production

Submitted by Administrator on 3 March, 2014 - 09:11

After an extended testing phase we have released the production version of LiceBase at the designated URL https://licebase.org as scheduled today. In this process we have also taken down the provisonal test-server for good. This means that the official version of LiceBase is also currently the only one. LiceBase is meant to evolve over time, so the functionality is likely to be extended in the future.

Currently the database contains the following data:

[NEWS] RNA-seq data added

Submitted by Administrator on 27 February, 2014 - 11:13

The new RNA-sequencing data covering various organs and copepodid stages have been added to the genome browser. You can activate them under Select Tracks -> Reads. The new tracks are marked with (HBR-1) to (HBR-10). Click on the [?] behind the track name to get more information about the content.

All reads provided by FASTERIS are single-end sequences from Illumina HiSeq, using a strand specific RNA-seq protocol (total RNA protocol, TruSeq v.2, with polyA selection). All libraries are un-normalized except for HBR-4N.

Problem with Internet Explorer [solved]

Submitted by Administrator on 23 February, 2014 - 21:31

There was a problem with LiceBase on Internet Explorer, the pages would render without any formatting ("black on white") and thereby become unusable. Some of you might have noticed.

By installing an add-on module we were able to overcome the bug in IE that causes this effect and the solution was tested with IE 9 (older versions might work as well but we neither recommend nor support them for use with LiceBase.)

Need ID for nauplius exp

Submitted by Sussie Dalvin on 14 January, 2014 - 11:11

Anybody putting in nauplius RNAi experiments: For now I have put them under the ID: Å, but this will be changed to have a more orderly way of putting them in.

Not able to create new RNAi entries

Submitted by Heidi Kongshaug on 9 January, 2014 - 15:33

I am not able to add new RNAi experiments.

Under RNAi folder I only have the option to view previous experiments.

GBrowse Error 500 [solved]

Submitted by Administrator on 16 October, 2013 - 15:11

The genome browser is not working TEST

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