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.

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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.