This directory contains the May 2005 Zv5 assembly of the zebrafish genome
(UCSC version danRer3) obtained from the Wellcome Trust Sanger Institute
and 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, Massachusetts.
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.
RepeatMasker open-3.0 version with RepBase libraries:
RepBase Update 9.04, RM database version 20040702 with the addition of
the zebunc.ref (Zebrafish Unclassified) repeats library from RepBase 9.06.
- scaffold*.fa.gz: gzip compressed FASTA sequence of individual scaffolds
for chrNA and chrUn. These are repeatmasked as described above.
- md5sum.txt - Checksum file.
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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/danRer3/chromosomes. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The Zv5 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/Zv5release/. 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.
Name Last modified Size Description
Parent Directory -
chr1.fa.gz 2005-08-04 14:56 17M
chr10.fa.gz 2005-08-04 14:56 12M
chr11.fa.gz 2005-08-04 14:56 13M
chr12.fa.gz 2005-08-04 14:56 11M
chr13.fa.gz 2005-08-04 14:56 14M
chr14.fa.gz 2005-08-04 14:56 21M
chr15.fa.gz 2005-08-04 14:56 14M
chr16.fa.gz 2005-08-04 14:57 16M
chr17.fa.gz 2005-08-04 14:57 15M
chr18.fa.gz 2005-08-04 14:57 16M
chr19.fa.gz 2005-08-04 14:57 22M
chr2.fa.gz 2005-08-04 14:57 15M
chr20.fa.gz 2005-08-04 14:57 17M
chr21.fa.gz 2005-08-04 14:57 12M
chr22.fa.gz 2005-08-04 14:57 15M
chr23.fa.gz 2005-08-04 14:57 17M
chr24.fa.gz 2005-08-04 14:57 10M
chr25.fa.gz 2005-08-04 14:57 8.7M
chr3.fa.gz 2005-08-04 14:57 14M
chr4.fa.gz 2005-08-04 14:57 10M
chr5.fa.gz 2005-08-04 14:57 22M
chr6.fa.gz 2005-08-04 14:57 9.9M
chr7.fa.gz 2005-08-04 14:57 18M
chr8.fa.gz 2005-08-04 14:57 13M
chr9.fa.gz 2005-08-04 14:57 13M
chrM.fa.gz 2005-08-04 14:57 5.3K
chrNA.fa.gz 2005-08-04 14:57 72M
chrUn.fa.gz 2005-08-04 14:57 54M
scaffoldNA.fa.gz 2005-08-04 14:59 72M
scaffoldUn.fa.gz 2005-08-04 14:59 54M
md5sum.txt 2005-08-04 15:36 1.3K