Solved: Image doesn`t show on In situ gallery overview

Submitted by Liv Sandlund on 11 December, 2014 - 16:28

Hi.

I`ve uploaded an in situ image but it does not show on the image gallery. What am I doing wrong?

Liv

Solved: Problems uploading gallery images

Submitted by Sussie Dalvin on 9 December, 2014 - 11:06

Hi,

I have problems uploading pictures for the gallery (RNAi). Some pictures goes in, but most fail. All pictures are taken with the same equipment on the same day and they are all jpeg

Todo-list for 2015, comments wanted

Submitted by Administrator on 3 December, 2014 - 09:58

The year 2014 has seen rapid progress in building sea lice genomics, most importantly, the final genome assembly and Ensembl annotation of the salmon louse genome is available to members of the Centre. We are now able to browse the genome, edit the annotation, upload and search experiments linked to genes in the genome and much more. Tons of - mainly RNA-seq data - have also been processed and uploaded to LiceBase. I would like to thank everyone who has contributed content to LiceBase, uploaded experiments, and provided feed-back. It's the valuable content that makes LiceBase a unique resource.

As this year comes to an end, we should make a list of things that will be attempted next year together with a prioritization of tasks. Extending the functionality of LiceBase, making it more user friendly while keeping up to date with Drupal and Tripal releases will be major tasks. Also, integration with other resources developed nationally and internationally will allow us to profit from our previous achievements. What is more, it is our aim to make LiceBase an open resource available to the general public together with the publication of a genome paper during next year.

Salmon genome BLAST database

Submitted by Administrator on 26 November, 2014 - 14:22

There is a new BLAST DNA database in the Blast section containing the latest whole genome shotgun assembly of Salmo salar.

Gene Ontology analysis of term enrichment for specific gene-sets

Submitted by Sussie Dalvin on 21 November, 2014 - 10:08

How do I use this, I get through to the revigo site and then what ??? Say I want to look at the group of genes that are enriched in legs versus the rest of the animal ?

Gene Ontology analysis of term enrichment for specific gene-sets:

All developmental stages vs. previous stage
All tissue specifc samples vs. all other tissues
Several interesting contrasts

Sequence is not correct

Submitted by Heidi Kongshaug on 12 November, 2014 - 15:26

EMLSAG00000011947 has several mistakes, which I have revealed by RACE PCR
It has an additional insert + the ending is wrong.

How to report it?
In "New Genome Annotation Erratum" the only evidence assay is RNA seq, and it is compulsory.
Or should I report it somewhere else?

Edit by Admin:
I have added a screenshot of the gene-model resulting from a GMAP alignment of the race product.
The exon/intron borders are in line with the newer RNA-seq evidence, but where not visible from the

[Update] Blast vs. Genome shows overlapping features

Submitted by Michael Dondrup on 6 November, 2014 - 09:49

I have updated the Blast server slightly, following Heidi's request:
When using BlastN or TBlastX vs. genomic scaffolds (LSalAtl2s masked and unmasked, but not "Everything L. Salmonis) the result page will list all genomic features that overlap with the location of the hit. This is very handy to test e.g. if primers or other short sequences hit the correct gene.

Details: this has not been implemented by making a new database with the gene sequences only. Instead the overlaps are computed from the annotation on the fly. This has several advantages:

Gbrowse

Submitted by Sussie Dalvin on 28 October, 2014 - 13:04

Problem resolved

Would like to BLAST predicted genes with nucleotide sequence

Submitted by Heidi Kongshaug on 20 October, 2014 - 10:50

I would like to BLAST primers that I make against predicted genes with a stable-ID.

[UPDATE] BLAST and BLAST downtime Monday

Submitted by Administrator on 11 October, 2014 - 10:38

BlastGraphicsViewer has been updated successfully. As a little goodie, the tree in the gene finding guide section on finding genes by sequence has been updated too. It now opens a new window with the correct Blast settings pre-set. If you are in doubt about which Blast settings to use, simply follow the decision process through the tree and click one of the green notes. Then paste in the search sequence.

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