Zebrafish 7.08.3 release
kj2 at sanger.ac.uk
Mon Aug 12 10:48:50 EST 2002
Zebrafish Data Update
We are pleased to announce the release of Zebrafish version 0.8.
This Ensembl website uses the sequences of clones out of
BAC/PAC libraries. The sequences were taken from a data freeze
from the 16th of July 2002 and comprise 36 Mb (2 percent of the
1.7 Gb zebrafish genome). This is nearly double the size of the
previous Zebrafish Ensembl database.
Note that this release is not based on the new whole genome
Ensembl mart has been updated with the Zebrafish data, and is now
The library used for repeat masking included the repbase zebrafish
library and an additional library which consists of:
- repeats Dr000001-Dr000409 identified by Zhirong Bao using his
Recon repeat identification software (Bao and Eddy, submitted).
This identifies the majority of repeats present more than 400 times
in zebrafish genome.
- repeats drr410-drr1225 identified by Rick Waterman (Johnson lab,
WashU) as individual examples of repeats (through BLAST
analysis of a 2% sample of zebrafish genome against the entire
zebrafish WGS database (~4,000,000 traces, data from spring
2002), and includes most repeats present greater than 50 times in
The repeat set is downloadable at
The EST assemblies generated by the Johnson lab at WashU
(http://zfish.wustl.edu/) have been included in the Blast analysis.
EPCR was used to map the zebrafish STS. Thes set included the
zebrafish STSs provided by ZFIN (http://zfin.org/cgi-
bin/webdriver?MIval=aa-ZDB_home.apg) and STSs derived from
BAC end sequencing and subsequent primer selection (Robert
Geissler, Tuebingen <robert.geisler at tuebingen.mpg.de>).
The data have been released to the FTP site and should be
available on the public mirror within a couple of hours:
Local Ensembl Installations - new/updated databases
Those wishing to update a local Ensembl installation should
download and install the following databases:
New FASTA dumps and flatfiles have been produced for Zebrafish
No new branch was required for this data - the website is still on the
ensembl-web on branch-ensembl-7-3
ensembl-api on branch-ensembl-7
You should, however, "cvs update" in htdocs, modules, and
ensembl-draw; and update your Danio_rerio.ini file appropriately.
More information about the Zbrafish