New zebrafish assembly Zv4 released

Kerstin Jekosch kj2 at sanger.ac.uk
Mon Jul 12 04:14:00 EST 2004


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The Sanger Institute (http://www.sanger.ac.uk) in Cambridge, UK, has 
release the fourth zebrafish genome assembly.

The Zv4 assembly comprises a total sequence length of 1,560,480,686 bp  in
21,333 supercontigs/scaffolds. Detailed Information about this  assembly
can be found at
http://www.sanger.ac.uk/Projects/D_rerio/Zv3_assembly_information.shtml 
and the data can be downloaded at
ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv4release.

We have also released a Zv4 pre-ensembl database
(http://pre.ensembl.org/Danio_rerio). Please note that these preliminary 
databases don't feature a gene build. The complete ensembl database is 
scheduled for release in September 2004.

Naming conventions

Supercontigs that could be tied to FPC contigs based on BAC end
placement were given the name 'Zv4_scaffold' followed by a random  number,
the other supercontigs were named 'Zv4_NA', again followed by a  random
number. Please note that the mapped supercontigs are not named  after the
corresponding numbers of fpc contigs anymore, as the fpc  database was and
will be undergoing name changes. Finished and
unfinished clone sequences were stitched into the supercontig sequence 
and the supercontigs placed onto chromosomes where possible. According  to
the agreement reached at the European zebrafish meeting in Paris,  2003,
we translated linkage group numbers directly into chromosome  numbers
(e.g. linkage group 1 = chromosome 1).

For more information on the project, please go to
http://www.sanger.ac.uk/Projects/D_rerio/





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