Welcome to the GAFFA Web Server for the GenoFisk project! GAFFA (Genome Annotation Framework for Flexible Analysis) is a framework for analysis, management, integration and storage of genomics data, developed at the CBU.
GenoFisk is a platform of the FUGE program for functional genomics, financed by the Norwegian Research Council . The purpose of GenoFisk is to increase our understanding of the biology of Atlantic cod (Gadus morhua) and Atlantic salmon (Salmo salar). This includes EST and genome sequencing, studies of specific functional genes and expression analysis.
This website provides a resource for searching, as well as manual and automatic annotation, of the transcriptome and genome data for Cod (Gadus morhua). In addition to being a valuable sequence resource in itself, a high quality assembly and annotation of the transcriptome is a critical resource for the annotation of the genome sequence for cod, that is currently being sequenced and analysed by the Norwegian Cod Genome Consortium, as a part GenoFisk.
A number of assemblies integrating cDNA sequences into contigs and singletons can be searched by BLAST annotations as well as automatic and manual CDS annotations. A BLAST service also allows searching the contigs by sequence similarity. Further, Transcript Libraries can be browsed and described.
The transcriptome data currently available includes:
- Sanger sequenced ESTs from the IMR, from NIFES and from Nofima in Norway.
- Sanger sequenced ESTs from the Atlantic Cod Genomics and Broodstock Development in Canada.
- cDNA sequenced using Pyrosequencing in connection to the Cod Genome Project.
- cDNA sequenced using Pyrosequencing from Bodo University College
- cDNA sequenced using Pyrosequencing from NIFES
Members of the Genofisk consortium and other contributing research groups are encouraged to use this resource and the data within it. Please contact as early as possible, and at the very least before submitting any derived results. The data found in GAFFA is not yet publicly released and any results derived from this may not be published, except with explicit permission from the GenoFisk Consortium and its partners. To find out more, or apply for an account, please send an email to firstname.lastname@example.org
We are working on extending and improving the GAFFA Web Server to add improved automated contig annotation and to integrate the resources of the Salmon Genome Project (SGP) .
The GmE100215, release candidate transcriptome assembly is now available.
The GmG091219, (release candidate one) genome assembly is now available.