This directory contains the March 2006 Zv6 assembly of the zebrafish genome
(UCSC version danRer4) 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 March 20 2006 (open-3-1-5) version with RepBase libraries:
RepBase Update 20060315, RM database version 20060315 with the addition
of the zebunc.ref (Zebrafish Unclassified) repeats library from
RepBase 11.02.
- scaffold*.fa.gz: gzip compressed FASTA sequence of individual scaffolds
for chrNA_random and chrUn_random. 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/danRer4/chromosomes. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The Zv6 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/Zv6release/. 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 -
md5sum.txt 2006-05-01 16:51 1.4K
chrM.fa.gz 2006-05-01 16:19 5.3K
scaffoldUn_random.fa.gz 2006-05-01 16:20 4.8M
chrUn_random.fa.gz 2006-05-01 16:19 4.9M
chr25.fa.gz 2006-05-01 16:19 12M
chr24.fa.gz 2006-05-01 16:19 14M
chr4.fa.gz 2006-05-01 16:19 14M
chr22.fa.gz 2006-05-01 16:18 15M
chr19.fa.gz 2006-05-01 16:18 16M
chr11.fa.gz 2006-05-01 16:18 16M
chr23.fa.gz 2006-05-01 16:19 16M
chr10.fa.gz 2006-05-01 16:18 17M
chr9.fa.gz 2006-05-01 16:19 17M
chr21.fa.gz 2006-05-01 16:18 17M
chr15.fa.gz 2006-05-01 16:18 18M
chr12.fa.gz 2006-05-01 16:18 18M
chr18.fa.gz 2006-05-01 16:18 18M
scaffoldNA_random.fa.gz 2006-05-01 16:20 18M
chr2.fa.gz 2006-05-01 16:18 19M
chr17.fa.gz 2006-05-01 16:18 19M
chr20.fa.gz 2006-05-01 16:18 19M
chr13.fa.gz 2006-05-01 16:18 20M
chrNA_random.fa.gz 2006-05-01 16:19 20M
chr16.fa.gz 2006-05-01 16:18 20M
chr8.fa.gz 2006-05-01 16:19 20M
chr6.fa.gz 2006-05-01 16:19 21M
chr1.fa.gz 2006-05-01 16:18 22M
chr3.fa.gz 2006-05-01 16:19 24M
chr5.fa.gz 2006-05-01 16:19 26M
chr7.fa.gz 2006-05-01 16:19 27M
chr14.fa.gz 2006-05-01 16:18 28M