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.

I will also add the ability to Blast against NT, NR and Swissprot, so that you can check you genes of interest for new hits directly from LiceBase. Please let me know if there are further database you require, and we'll install them asap.

The BLAST results are displayed in a user friendly graphical format with links. If you blast against the genome assembly DNA sequence, you can inspect the hit region in GBrowse. Under each HSP you will find a link like this one: Open region in GBrowse. If you click on it, the region of the alignment will open in a new window in your browser.
Each genomic feature now also displays a link in its Resource menue: Run BLAST search. This link allows to BLAST the sequence of this feature directly, by filling out the BLAST search form for you.

Access restrictions apply like always: you need to have a log-in for LiceBase to use BLAST.

Create and edit new genomic features

All your sequences belongs to us!

We want to collect all the hidden sequences and wisdom that is collected in your drawers, Drive X:\, or Excel sheets, at least as long as they are verified salmon louse sequences or annotated genes or otherwise highly important but missing or incomplete in the reference assembly. The aim is to improve the genome sequence and annotation.

To accomplish this epic task, we have improved the editing and creation of genomic features. It is now possible to add genes, transcripts, PCR-primers and other sequences to the database, and position them relative to existing reference assembly. To add a new feature to the database, find the link in your menu:

Any user who has the role "Annotator" (that's most of you) can upload new sequence features.

When you fill in this for for a new feature, please fill in the mandatory fields: Name, Unique Name, Title, and Feature Type, and most important, copy-paste the sequence into the Residues: field. You may also add a good description. Don't worry if you do not know the feature localization (feature 5' MIN, source feature). After saving the sequence, you can use BLAST to localize the feature in the assembly.

If the sequence is very short (e.g.