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.

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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/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.