This directory contains the Apr. 2004 freeze of the D. yakuba genome 
(droYak1) from the Genome Sequencing Center at Washington University 
School of Medicine in St. Louis. 

Files included in this directory:

droYak1.2bit - contains the complete D. yakuba/droYak1 genome sequence
    in the 2bit file format.  While we are providing the .2bit for
    this assembly, we will continue to use the .nib files in
    the Genome Browser.  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.zip - Description of how the working draft was generated from
    fragments at a chromosome layout level. 

chromFa.zip - The working draft sequence chromosome in one file per
    chromosome.  Repeats from RepeatMasker and Tandem Repeats Finder
    (with period of 12 or less) are in lower case while non-repeating
    sequence is in upper case.  RepeatMasker March 2004 version with
    RepBase libraries: RepBase Update 8.4, RM database version
    20040225

chromFaMasked.zip - The working draft sequence in one file per
    chromosome. Repeats are masked by capital N's and non-repeating
    sequence is shown in upper case.

chromOut.zip - RepeatMasker .out file for chromosomes.  These were done
    with RepeatMasker at the -s sensitive setting.

chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file 
    per chromosomes.  

est.fa.gz - D. yakuba ESTs in GenBank. This sequence data is updated once a 
    week via automatic GenBank updates.

ms5sum.txt - Checksums of files in this directory.

mrna.fa.gz - D. yakuba mRNA from GenBank. This sequence data is updated 
    once a week via automatic GenBank updates.

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.


droYak1.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/droYak1/bigZips. To download multiple files, 
use the "mget" command:

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

The D. yakuba sequence is made freely available before scientific 
publication by The Genome Sequencing Center, WUSTL School of Medicine 
with the following understanding: 

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases. 
2. Users are free to use the data in scientific papers analyzing particular 
   genes and regions if the providers of these data (Genome Sequencing 
   Center, WUSTL School of Medicine) are properly acknowledged. 
3. The Drosophila yakuba analysis group is aiming to publish an initial 
   analysis of the D. yakuba genome sequence in 2005 (submitted in early 
   2005) that will include descriptions of the assembly, genome landscape, 
   comparative analysis and initial gene content. People who would like to 
   coordinate other genome-wide analysis with this work should contact 
   Richard K. Wilson, Genome Sequencing Center Director, Washington 
   University School of Medicine. We welcome a coordinated approach to 
   describing this community resource. 
4. Any redistribution of the data should carry this notice.