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,
Massachusetts.
For more information on the zebrafish genome, see the project website:
http://www.sanger.ac.uk/Projects/D_rerio/
Files included in this directory:
danRer5.2bit - contains the complete zebrafish/danRer5 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
danRer5.agp.gz - Description of how the assembly was generated from
fragments.
danRer5.fa.gz - "Soft-masked" assembly sequence in one file.
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.
danRer5.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
danRer5.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. 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).
danRer5.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
est.fa.gz - Zebrafish ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
md5sum.txt - checksums of files in this directory
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.
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.fa.gz - Same as upstream1000, but 2000 bases.
upstream5000.fa.gz - 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.
danRer5.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 that 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/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
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.
Name Last modified Size Description
Parent Directory -
danRer5.2bit 2007-09-05 08:54 364M
danRer5.agp.gz 2007-09-11 22:03 101K
danRer5.chrom.sizes 2007-08-24 15:00 81K
danRer5.fa.gz 2007-09-11 22:11 443M
danRer5.fa.masked.gz 2007-09-11 22:15 242M
danRer5.fa.out.gz 2007-09-11 22:03 105M
danRer5.trf.bed.gz 2007-09-11 22:04 8.8M
est.fa.gz 2019-10-17 00:07 305M
est.fa.gz.md5 2019-10-17 00:07 44
genes/ 2020-02-05 13:46 -
md5sum.txt 2014-01-03 15:15 304
mrna.fa.gz 2019-10-17 00:01 18M
mrna.fa.gz.md5 2019-10-17 00:01 45
refMrna.fa.gz 2019-10-17 00:07 12M
refMrna.fa.gz.md5 2019-10-17 00:07 48
upstream1000.fa.gz 2019-10-17 00:08 4.1M
upstream1000.fa.gz.md5 2019-10-17 00:08 53
upstream2000.fa.gz 2019-10-17 00:08 7.8M
upstream2000.fa.gz.md5 2019-10-17 00:08 53
upstream5000.fa.gz 2019-10-17 00:08 19M
upstream5000.fa.gz.md5 2019-10-17 00:08 53
xenoMrna.fa.gz 2016-03-14 05:17 5.0G
xenoMrna.fa.gz.md5 2016-03-14 05:17 49
xenoRefMrna.fa.gz 2019-10-17 00:07 319M
xenoRefMrna.fa.gz.md5 2019-10-17 00:07 52