This directory contains the Oct. 2004 assembly of the fugu genome
(fr2, JGI V4.0), as well as repeat annotations and GenBank sequences.

This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the fugu genome, see the project website:
	http://genome.jgi-psf.org/Takru4/Takru4.info.html
	http://www.fugu-sg.org/

Files included in this directory:

fr2.2bit - contains the complete fugu/fr2 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
    scaffolds, unpacking to one file per chromosome, chrUn and chrM.

chromFa.tar.gz - The assembly sequence in one file per chromosome.
    Repeats from WindowMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.  Note, this sequence is *not* masked with
    the RepeatMasker .out specification.

chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
    Gaps and Repeats are masked by capital Ns; non-repeating sequence is
    shown in upper case.

chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
    RepeatMasker was run with the -s (sensitive) setting.
    RepeatMasker version: October 6, 2006 (open-3-1-6)
    with RepBase libraries: RepBase Update 20061006.

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format (one file per chromosome).

chromWMSdust.bed.tar.gz - per-chrom bed files used as repeat areas
	identified by WindowMasker with the -sdust option.

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

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Fugu 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.

fr2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

fr2.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

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If you plan to download a large file or multiple files from this 
directory, we recommend that 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/fr2/bigZips. To download multiple 
files, use the "mget" command:

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

1.  These data have been freely provided by the JGI for use in the
	UCSC Genome Browser.