Zebrafish 7.08.3 release

Kerstin Jekosch 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 
shotgun
assembly.

Ensembl mart has been updated with the Zebrafish data, and is now
ensembl_mart_7_4

Data Details
============

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 genome.  

The repeat set is downloadable at
http://www.genetics.wustl.edu/fish_lab/repeats/.

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>).  

Data Availability
=================

The data have been released to the FTP site and should be 
available on the public mirror within a couple of hours:  

ftp://ftp.ensembl.org/pub/Danio_rerio

Local Ensembl Installations - new/updated databases
=================================================
==

Those wishing to update a local Ensembl installation should 
download and install the following databases:  

danio_rerio_core_7_08
danio_rerio_maps_7_08
danio_rerio_lite_7_08

ensembl_mart_7_4

New FASTA dumps and flatfiles have been produced for Zebrafish 
as well.  

Software Updates
================

No new branch was required for this data - the website is still on the
following branches:

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 mailing list