This directory contains the Jan. 2007 assembly of the C. briggsae genome
(cb3), as well as repeat annotations and GenBank sequences.

This assembly was produced by Washington University in St. Louis (WUSTL) School 
of Medicine Genome Sequencing Center and the Sanger Institute. For more 
information on the C. briggsae genome, see the WUSTL project website at
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+briggsae.
The sequence data may also be downloaded from:
ftp://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_briggsae/assembly/Caenorhabditis_briggsae-1.0/output/chromosomes.

Files included in this directory:

cb3.2bit - contains the complete C. briggsae/cb3 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.  The main assembly is found in the chrN.fa
    files, where N is the name of the chromosome. The chrN_random.fa
    artificial chromosome files contain clones that are not yet finished
    or cannot be placed with certainty at a specific place on that chromosome.
    The chrUn artifical chromosome contains clones that are not yet finished,
    and can not be oriented or assigned to any chromosome.

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 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).

est.fa.gz - C. briggsae 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 - C. briggsae 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.

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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/cb3/bigZips. To download multiple 
files, use the "mget" command:

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

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The C. briggsae sequence is made freely available to the community by the
Genome Sequencing Center at the WUSTL School of Medicine. Please see the
WUSTL data use policy at http://genome.wustl.edu/data.cgi for data use
restrictions and citation information.