Blogs

New gene finding guide

Submitted by on

Hi all,

we have a new gene finding guide. This guide is a summary of  the efforts made during the course. The most common use-case is to find your genes of interest in the annotation. The documentation should serve as a reminder and guidance to the different possible steps to discover your genes in the new assembly. Please have a look at the guide at:

https://licebase.org/finding_genes

Feature search updated

Submitted by on

The search mask for sequence features has been updated. It now allows to search for genomic features by their annotation. A few genes from the annotation have received human readable annotations, e.g. 'Putative chitinase' in addition to their Ensembl gene ids (EMLSAG).

These annotation properties can now be searched for by entering a search phrase into the "Search annotation text" field. This search is case sensitive. Annotations can be stored as different annotations properties, default for human readable is "Note".

NEWS: Documentation and Updates of the week

Submitted by on

Documentation and Data-Quality incentive

As a part of our initiative for improved data quality and documentation I have started to write a series of documents as guidelines for how to annotate experiments and how to use LiceBase for various tasks. The first outcome of this is the RNAi-checklist. Following the checklist should help you to make better annotations for your experiments. This incentive should help every user of LiceBase to be able to extract essential information for data-mining and reproduction of annotated experiments, and should allow to draw the a better connection between gene knock-down and phenotypes. Everyone working with RNAi is invited to read and comment on this check-list and propose changes. In addition, we have improved and rewritten parts of the documentation embedded into the RNAi submission form. 

Error message: about incorrect target ID in edit RNAi

Submitted by on

Hei ,

prøver å oppdatere basen men får feilmelding om at dette ikke er en riktig target id EMLSAP00000008531

trying to update my experiment but I am getting an error that EMLSAP00000008531 is not a correct Target ID.

  • Primary target ID: found no valid post with that title.

If you see this message, most likely the Target ID was not valid. A full Target ID looks like this:

LiceBase Presentation and Demo Life at SeaLice 2014

Submitted by on

We are proud to present LiceBase to the global sea lice research community at the SeaLice 2014 conference in Portland, Maine. The presentation of LiceBase takes place today, Sept. 2. There will also be a life demonstration for an interested audience on Sept. 3 in the afternoon (time to be announced). There are a lot of highly interesting talks on sea lice biology today, which depict the use of genomic resources of sea lice that are also available in LiceBase. There are several keys to sustainable sea lice control in its genome some of which are presented today.

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

Submitted by on

"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").

News: BLAST and other major updates

Submitted by on

As you might have seen already, the start page has been revamped by adding icons for the most important tasks to make them easier to find.

BLAST

The most important update is the introduction of a BLAST server (https://licebase.org/blast) inside of LiceBase. It allows to run brief Blast queries against the genome reference assembly sequence, predicted proteins and other useful databases including all ESTs from Genbank and the old Consensus Clusters and IMR ESTs and the Calanus Finmarchicus transcriptome assembly.

Pages

Subscribe to RSS - blogs