23.10.2007

We have now uploaded 22.672 EST's to the GenBank. Out of a total number of 29.018 sequences, we were left with with 22.672 after removing mitochindrial sequences, vector sequences and a general quality check. Please find more inforamtion regarding the different cDNA libraries below:

Name: Gadus morhua pooled liver samples SSH library (exposed to toxicants) ZNL
Total ESTs: 2304
Passed: 2004 (86%)
Average length:613

Name: Gadus morhua stem cell library ZNS
Total ESTs: 3935
Passed: 2719 (69%)
Average length:442

Name: Gadus morhua pooled liver samples library (exposed to toxicants) GML
Total ESTs: 4608
Passed: 4002 (86%)
Average length:593

Name: Gadus morhua intestinal library ZNC
Total ESTs: 3456
Passed: 3153 (91%)
Average length:563

Name: Gadus morhua pooled liver samples library KL
Total ESTs: 426
Passed: 410 (96%)
Average length:512

Name: Gadus morhua pooled kidney samples library ZNKAA
Total ESTs: 7353
Passed: 5408 (73%)
Average length:492

Name: N/A
Total ESTs: 10
Passed: 4 (40%)
Average length:621

Name: Gadus morhua pooled gill samples library ZNGAA
Total ESTs: 6879
Passed: 4924 (71%)
Average length:481

Name: Gadus morhua liver and intestine library TSTf
Total ESTs: 56
Passed: 47 (83%)
Average length:461

5.2.2007

Sekvensering av stress-responsive gener hos torsk. Fakta-ark Havbruk, Norges forskningsråd (Norwegian Research Council) (in Norwegian).

Finner torskens stressgener. Fra brosjyren Bærekraft og Innovasjon i blått og grønt, Norges forskningsråd (Norwegian Research Council) (in Norwegian).

18.10.2006

We are now printing our first array's. A gene name list can be downloaded here.

30.3.2006

Our new PhD student Kai K. Lie, hired from June 2005 - June 2008 in this project, is here seen at the Havbruk 2006 conference arranged in Bergen March 2006.

28.03.2006

A pipeline for automatic EST annotation has been established in collaboration with CBU. It's based on a triplicate BLAST system; BLASTX (protein) - BLASTN (nucleotide) - BLASTN (EST). Both best hit and best annotated hit are reported for protein and nucleotide BLAST's. That way we don't have to screen through hundreds of un-annotated Tetraodon and Danio sequences uploaded to the Genbank. Our database has also been made searchable, in that we can run BLASTN against our own sequences. These include about 15000 EST's, that consist of 1300 contigs and about 10000 singlets (representing 11300 genuine gene sequences). Unfortunately, the database will not be made public in so far. But if you are interested in certain genes, I can search for them within the database for you. And provide them upon request (and within an agreement on the use).

The pipeline will be presented on a poster at the Havbruk 2006 conference in Bergen 29-31 March 2006.

14.2.2006

We have now assembled our 15.000 cod EST's with the automated annotation pipeline developed by the Computational Biology Unit (CBU) at the University of Bergen. A lot of interesting genes have been found. Soon we will start uploading these gene sequences to the GenBank. We have also started the process of selecting the EST's to be included on our custom-made array.

5.1.2006

We have now sequenced about 10000 EST clones from two cDNA libraries, one from gill tissue and one from kidney tissue. The sequences will be uploaded to the GenBank as soon as possible. They will also be used in assembly with the other 5000 EST sequences we have, in search for stress-related genes, to be used in array production.