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The assemblies are based on a whole genome shotgun assembly merged with information from the physical map and (un-)finished clone sequences. This is done by using the placement of the BAC ends, ESTs, markers and clone sequence homology to link the assembly supercontigs to the FPC contigs and the clones within. Whole genome shotgun contigs and clone sequences are then arranged into new contigs on the appropriate chromosomes. This process will improve the presented genome sequence continuously with every release until eventually all whole genome shotgun derived sequence can be replaced by high quality finished sequence data.
As soon as an integrated assembly is completed, a pre-EnsEMBL database (http://pre.ensembl.org/Danio_rerio/) with the sequence information and sequence features like BLAST homologies, best-in-genome EST/cDNA placement, etc. is generated. Once the gene build is completed on a new assembly, it will progress to a full EnsEMBL database (http://www.ensembl.org/Danio_rerio/), thereby replacing the previous assembly. A full EnsEMBL database doesn't only differ from a pre-EnsEMBL by displaying genes, but also offers comparison to the genome sequence of other EnsEMBL species, ortholog predictions, SNP mapping and the search tool EnsMART (http://www.ensembl.org/Multi/martview). The EnsEMBL databases are updated monthly in order to reflect changes in the underlying database structure and code.
The zebrafish homepage guides you to all assembly related web pages at http://www.sanger.ac.uk/Projects/D_rerio/wgs.shtml
On this page you can find links to e.g.
- the pre-EnsEMBL database with the latest assembly (in case there is one upcoming) http://pre.ensembl.org/Danio_rerio/
- BLAST/SSAHA search of pre-EnsEMBL data http://pre.ensembl.org/Multi/blastview?species=Danio_rerio
- the EnsEMBL database http://www.ensembl.org/Danio_rerio/
- BLAST/SSAHA search of EnsEMBL data http://www.ensembl.org/Multi/blastview?species=Danio_rerio
- the comprehensive search tool EnsMART http://www.ensembl.org/Multi/martview
- download the assemblies at ftp://ftp.ensembl.org/pub/assembly/zebrafish
- assembly information at http://www.sanger.ac.uk/Projects/D_rerio/Zv4_assembly_information.shtml (replace 'Zv4' by the assembly you are interested in)