This directory contains the Jul. 2007 Zv7 assembly of the zebrafish genome
(danRer5) obtained from the Wellcome Trust Sanger Institute, as well as
repeat annotations and GenBank sequences.
This assembly was produced by a collaboration between the
Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute
for Developmental Biology in Tuebingen, Germany, the Netherlands Institute
for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands
and Yi Zhou and Leonard Zon from the Children's Hospital in Boston,
For more information on the zebrafish genome, see the project website:
Files included in this directory:
- chr*.fa.gz: gzip compressed FASTA sequence of each chromosome.
Repeats (from RepeatMasker and Tandem Repeat Finder)
are in lower case while non-repeating sequence is in upper case.
May 17 2007 (open-3-1-8) version of
RepeatMasker with the RepeatMasker library RELEASE 20061006. The
RepeatMasker library included the addition of repeats from the
zebunc.ref (Zebrafish Unclassified) repeats library from RepBase12.07
from the Genetic Information Research Institute (GIRI). Some repeats were
removed from zebunc.ref because they mask out real genes (see the
danRer5 RepeatMasker track description page for more details).
- unmappedScaffolds.fa.gz: gzip compressed FASTA sequence of all the
unmapped scaffolds. These are repeatmasked as described above.
- md5sum.txt - Checksum file.
If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/danRer5/chromosomes. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The Zv7 zebrafish sequence data were produced by the Zebrafish Sequencing
Group at the Sanger Institute and can be obtained directly from
ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release/. All sequence data
are made available before scientific publication with the understanding that
the groups involved in generating the data intend to publish the initial
large-scale analyses of the dataset. This will include a summary detailing
the data that have beeen generated and key features of the genome identified
from genomic assembly and clone mapping/sequencing. Any redistribution of
the data should carry this notice.
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