This directory contains the March 2006 Zv6 freeze of the zebrafish genome
(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:
danRer4.2bit - contains the complete zebrafish/danRer4 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 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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case.
chromOut.tar.gz - RepeatMasker .out file for chromosomes. These were created
by RepeatMasker at the -s sensitive setting.
chromTrf.tar.gz - 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
nightly via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated nightly via automatic GenBank
updates.
scaffoldRandomsFa.tar.gz - Individual scaffold sequences in two files. There
is one file for the chrNA_random scaffolds and one file for the
chrUn_random scaffolds. Masking is the same as for chromFa.tar.gz.
Repeats are shown in lower case; 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.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 nightly via automatic
GenBank updates.
danRer4.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/danRer4/bigZips. 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 -
chromAgp.tar.gz 2007-03-29 10:49 162K
chromFa.tar.gz 2007-03-29 10:57 497M
chromFaMasked.tar.gz 2007-03-29 11:01 273M
chromOut.tar.gz 2007-03-29 10:50 117M
chromTrf.tar.gz 2006-05-01 14:40 9.0M
danRer4.2bit 2006-04-23 13:24 447M
danRer4.chrom.sizes 2006-04-23 13:21 422
danRer4.fa.gz 2020-01-23 02:21 497M
est.fa.gz 2019-10-17 00:17 305M
est.fa.gz.md5 2019-10-17 00:17 44
md5sum.txt 2013-12-10 13:59 360
mrna.fa.gz 2019-10-17 00:11 18M
mrna.fa.gz.md5 2019-10-17 00:11 45
refMrna.fa.gz 2019-10-17 00:17 12M
refMrna.fa.gz.md5 2019-10-17 00:17 48
scaffoldRandomsFa.tar.gz 2006-05-01 14:40 23M
upstream1000.fa.gz 2019-10-17 00:18 4.0M
upstream1000.fa.gz.md5 2019-10-17 00:18 53
upstream2000.fa.gz 2019-10-17 00:18 7.7M
upstream2000.fa.gz.md5 2019-10-17 00:18 53
upstream5000.fa.gz 2019-10-17 00:18 19M
upstream5000.fa.gz.md5 2019-10-17 00:18 53
xenoMrna.fa.gz 2016-03-14 06:54 5.0G
xenoMrna.fa.gz.md5 2016-03-14 06:54 49
xenoRefMrna.fa.gz 2019-10-17 00:17 319M
xenoRefMrna.fa.gz.md5 2019-10-17 00:17 52