This directory contains the Nov. 2003 Zv3 freeze of the zebrafish genome 
(danRer1) 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:

chromAgp.zip - Description of how the assembly was generated from
     fragments, unpacking to one file per chromosome.  

chromFa.zip - 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 January 2004 version with
    RepBase libraries: RepBase Update 8.4, RM database version
    20040225.

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.

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.


danRer1.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/danRer1/bigZips. To download multiple files, 
use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

The Zv3 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/Zv3release/. 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.