This directory contains the June 2004 Zv4 assembly of the zebrafish genome 
(UCSC version 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.

Files included in this directory:

  - chr*.fa.zip: compressed FASTA sequence of each chromosome.
    Repeats (from RepeatMasker and Tandem Repeat Finder) 
    are in lower case while non-repeating sequence is 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.

  - md5sum.txt - Checksum file.

NOTE: chr1.fa.zip was replaced with chr1New.fa.zip on 06/06/05 because
chr1.fa was found to be incompletely repeat-masked. This problem has been 
corrected in chr1New.fa.zip. 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. 

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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/chromosomes. 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. 

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