This directory contains the May 2005 Zv5 freeze of the zebrafish genome
(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:
danRer3.2bit - contains the complete zebrafish/danRer3 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
chromAgp.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome. Repeats
from RepeatMasker and Tandem Repeats Finder (with period of 12 or less)
are shown in lower case; non-repeating sequence is shown in upper case.
RepeatMasker open-3.0 version with RepBase libraries: RepBase Update 9.11,
RM database version 20050112 with the addition of the zebunc.ref
(Zebrafish Unclassified) repeats library from RepBase 10.04.
chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats
are masked by capital Ns; non-repeating sequence is shown in upper case.
chromOut.zip - RepeatMasker .out file for chromosomes. These were created
by RepeatMasker at the -s sensitive setting.
chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into one
.bed file per chromosomes.
est.fa.gz - Zebrafish ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - MD5 checksum of these files to verify correct transmission.
mrna.fa.gz - Zebrafish mRNA from GenBank. This sequence data is updated once
a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
scaffoldUnsFa.tar.gz - Individual scaffold sequences with one file for each of
chrUn and chrNA scaffolds. Masking is the same as for chromFa.tar.gz.
Repeats are shown in lower case; non-repeating sequence is shown in
upper case.
scaffoldUnsFaMasked.tar.gz - Individual scaffold sequences with one file for
each of chrUn and chrNA scaffolds. Repeats are masked by capital Ns;
non-repeating sequence is shown in upper case.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the RefSeq data which is updated daily for most
assemblies.
upstream2000.zip - Same as upstream1000, but 2000 bases.
upstream5000.zip - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
danRer3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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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/bigZips. 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 -
chromAgp.tar.gz 2005-08-04 11:24 375K
chromFa.tar.gz 2005-08-04 11:32 493M
chromFaMasked.tar.gz 2005-08-04 11:38 272M
chromOut.tar.gz 2005-08-04 11:25 117M
chromTrf.tar.gz 2005-08-04 11:39 8.9M
danRer3.2bit 2005-06-15 17:13 416M
danRer3.chrom.sizes 2005-06-16 14:07 409
danRer3.fa.gz 2020-01-23 02:20 494M
est.fa.gz 2019-10-17 00:30 305M
est.fa.gz.md5 2019-10-17 00:30 44
md5sum.txt 2014-02-03 11:34 417
mrna.fa.gz 2019-10-17 00:24 18M
mrna.fa.gz.md5 2019-10-17 00:24 45
refMrna.fa.gz 2019-10-17 00:30 12M
refMrna.fa.gz.md5 2019-10-17 00:30 48
scaffoldUnsFa.tar.gz 2005-08-04 11:34 125M
scaffoldUnsFaMasked.tar.gz 2005-08-04 11:39 66M
upstream1000.fa.gz 2019-10-17 00:31 3.9M
upstream1000.fa.gz.md5 2019-10-17 00:31 53
upstream2000.fa.gz 2019-10-17 00:31 7.5M
upstream2000.fa.gz.md5 2019-10-17 00:31 53
upstream5000.fa.gz 2019-10-17 00:32 18M
upstream5000.fa.gz.md5 2019-10-17 00:32 53
xenoMrna.fa.gz 2016-03-14 08:38 5.0G
xenoMrna.fa.gz.md5 2016-03-14 08:38 49
xenoRefMrna.fa.gz 2019-10-17 00:30 319M
xenoRefMrna.fa.gz.md5 2019-10-17 00:30 52