Blogs

News: Reporting Tool for Annotation Errata

Most human made systems and artifacts involve errors and mistakes (e.g. computer software); even more so in case of automatic predictions like weather forecasts, or even our genome annotation, even though it is by far the most reliable resource of gene annotation for L. salmonis and all sea lice that exists to date (albeit ESTs, tentative consensus). As errors cannot be completely avoided, we need ways to handle them in an appropriate manner. The first step of error management is to adequately report possible issues in our genome annotation.

News: Added Raw-data downloads, publications and other goodies

We have added several new and usefull features mainly to be found on the Organism pages:

  • Publications: we are now regularly importing new publications on L. salmonis from PubMed. These can be searched directly from Search Publications or are linked from the salmon louse organism page. The import runs automatically every 14 days. You can also create your own publications should we be missing one.

[IMPORTANT] Mandatory Primary Target ID in RNAi

We have made the field Primary Target ID mandatory in the RNAi experiment form, effective from today. We now have a very stable and high quality genome annotation, and I am highly convinced that annotating experiments with ENSEMBL stable IDs is highly superior to generic ids, especially when targeting a broader audience as users of LiceBase. There are several reasons for this: 

[NEWS] New tracks with all ESTs and consensus clusters

We have aligned all available mRNA sequences from Genbank, as well as the old consensus clusters (mainly CL-id contigs (CL123Contig1, etc.) but also singletons) and the masked ESTs (FN-ids and others) to the genome using GMAP. These are available as three new browser tracks. These tracks can be enabled in the GenomeBrowser under Select Tracks. The Genbank ESTs show a link to their genbank entry on click.

Here is an example display:

[News] New tracks and minor changes to the genome Browser

There are two new RNA-seq coverage tracks, both from virus infected glands, with IDs VP1 and VP2.

Also, there is a slight improvement, by linking back from the browser into licebase.

In the "Ensembl Genes" track, if you click on a gene, a ballon will pop up with two links:

  • Show details  
  • View Gene in LiceBase

Clicking on the second link will open the gene in LiceBase directlyt so you get the sequence, Blast hits and other annotation without the need to search.

[NEWS] KEGG pathway annotation imported

Results from a run of Pathway reconstruction using KEGG Automatic Annotation Server KAAS, have been uploaded to LiceBase. KAAS 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. EMLSAP00000004643) using 

Search Biological Data

[NEWS] Calanus finmarchicus homologs

A transcriptome shotgun assembly from RNA-seq data of  Calanus finmarchicus, an abundant zooplanktonic copepod crustacean in the northern Atlantic has been published recently [1].

We have run tblasn of all predicted L. salmonis protein sequences against the assembly contigs of C. finmarchicus downloaded from Genbank. The Blast results are available for each gene in its gene report menu under 

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