This directory contains the June 2004 Zv4 assembly of the zebrafish genome
(UCSC version danRer2) 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.zip: 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.
- md5sum.txt - Checksum file.
NOTE: chr1.fa.zip was replaced with chr1New.fa.zip on 06/06/05 because
chr1.fa was found to be incompletely repeat-masked. This problem has been
corrected in chr1New.fa.zip. This problem has been corrected in
chr1New.fa.zip, found in the danRer2/chromosomes directory. chromOut.zip
contains a new chr1New.fa.out RepeatMasker file in which an erroneous line in
the output has been removed. The Blastz alignments, Human Proteins tBLASTn and the Blat alignments of the ESTs, mRNAs, Affymetrix probe consensus sequences,
BAC ends and Radiation Hybrid Map sequences were all created using the
incompletely masked chromosome 1.
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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/danRer2/chromosomes. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
The Zv4 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/Zv4release/. 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.zip 2004-12-14 09:12 17M
chr1New.fa.zip 2005-06-06 19:22 18M
chr2.fa.zip 2004-12-14 09:18 16M
chr3.fa.zip 2004-12-14 09:22 13M
chr4.fa.zip 2004-12-14 09:22 10M
chr5.fa.zip 2004-12-14 09:23 20M
chr6.fa.zip 2004-12-14 09:23 9.9M
chr7.fa.zip 2004-12-14 09:24 19M
chr8.fa.zip 2004-12-14 09:25 11M
chr9.fa.zip 2004-12-14 09:25 13M
chr10.fa.zip 2004-12-14 09:12 11M
chr11.fa.zip 2004-12-14 09:13 11M
chr12.fa.zip 2004-12-14 09:13 10M
chr13.fa.zip 2004-12-14 09:14 11M
chr14.fa.zip 2004-12-14 09:14 18M
chr15.fa.zip 2004-12-14 09:15 11M
chr16.fa.zip 2004-12-14 09:15 13M
chr17.fa.zip 2004-12-14 09:16 13M
chr18.fa.zip 2004-12-14 09:17 14M
chr19.fa.zip 2004-12-14 09:17 15M
chr20.fa.zip 2004-12-14 09:19 18M
chr21.fa.zip 2004-12-14 09:19 12M
chr22.fa.zip 2004-12-14 09:20 11M
chr23.fa.zip 2004-12-14 09:20 13M
chr24.fa.zip 2004-12-14 09:21 7.6M
chr25.fa.zip 2004-12-14 09:21 7.7M
chrM.fa.zip 2004-12-14 09:25 5.5K
chrNA.fa.zip 2004-12-14 09:29 89M
chrUn.fa.zip 2004-12-14 09:31 51M
md5sum.txt 2005-06-06 19:24 1.3K