This directory contains the June 2004 Zv4 freeze of the zebrafish genome
(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.
NOTE: chr1.fa in chromFa.zip and chr1.fa.masked in chromFaMasked.zip were
replaced with chr1New.fa and chr1New.fa.masked, respectively, on 06/06/05
because the original chr1.fa was found to be incompletely repeat-masked.
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.
Files included in this directory:
chromAgp.zip - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.zip - [See NOTE above] 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 9.04, RM database version 20040702 with the
addition of the zebunc.ref (Zebrafish Unclassified) repeats library from
RepBase 9.06.
chromFaMasked.zip - [See NOTE above] The assembly sequence in one file per
chromosome. Repeats are masked by capital Ns; non-repeating
sequence is shown in upper case.
chromOut.zip - [See NOTE above] 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.
upstream1000.zip - Sequences 1000 bases upstream of annotated
transcription start of RefSeq genes. This includes only the
cases where the transcription start is annotated separately
from the coding region start. Note that upstream files are
generated only when an assembly is released. Therefore, the
data may be slightly out of synch with the RefSeq data in
assemblies that are incrementally updated nightly.
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.
danRer2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
-----------------------------------------------------------------
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/bigZips. 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 -
chromAgp.zip 2005-04-25 10:25 492K
chromFa.zip 2005-06-06 18:55 466M
chromFaMasked.zip 2005-06-06 19:15 264M
chromOut.zip 2005-06-06 18:48 110M
chromTrf.zip 2004-12-14 09:03 7.9M
danRer2.chrom.sizes 2004-12-02 14:53 409
est.fa.gz 2008-09-10 17:30 289M
md5sum.txt 2005-06-06 19:23 519
mrna.fa.gz 2008-09-10 17:07 16M
refMrna.fa.gz 2008-09-10 17:31 9.4M
upstream1000.zip 2004-12-14 09:04 1.3M
upstream2000.zip 2004-12-14 09:05 2.5M
xenoMrna.fa.gz 2008-09-10 17:12 686M