This directory contains the Mar. 2005 freeze of the C. intestinalis
genome (ci2) from the US DOE Joint Genome Institute (JGI).

Files included in this directory:

ci2.2bit - contains the complete C. intestinalis/ci2 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

ScaffoldFa.zip - The assembly sequence in one file per scaffold.
    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 version development-$Id: RepeatMasker,v 1.9 2005/05/04 
    18:27:42.

ScaffoldFaMasked.zip - The assembly sequence in one file per 
    scaffold. Repeats are masked by capital Ns; non-repeating 
    sequence is shown in upper case.  

ScaffoldOut.zip - A single RepeatMasker .out file for scaffolds. These were 
    created by RepeatMasker at the -s sensitive setting.

ScaffoldTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, and collected into one file.

md5sum.txt - MD5 checksum of the previous four files to verify 
    correct transmission.

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

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

refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
    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.


ci2.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/ci2/bigZips. To download multiple files, use
the "mget" command:

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

The C. intestinalis sequence is made freely available by JGI. For
restrictions on the use of these data, see the JGI Data Release
Policy at http://genome.jgi-psf.org/ciona4/ciona4.download.html.