This directory contains the Dec. 2002 freeze of the C. intestinalis
genome (ci1) from the US DOE Joint Genome Institute (JGI).

Files included in this directory:

ci1.2bit - contains the complete C. intestinalis/ci1 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

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 January 2004 version with
    RepBase libraries: RepBase Update 8.4, RM database version
    20040225.

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 - 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 translated into one 
    .bed file per scaffold.  

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

md5sum.txt - MD5 checksum of these files to verify correct transmission.

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

refMrna.zip - RefSeq mRNA from the same species as the genome.

xenoMrna.zip - All GenBank mRNAs from species other than that of 
    the genome.


ci1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

---------------------------------------------------------------
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/ci1/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.

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 2.9K 
[TXT]README.txt.bak06-May-2014 16:00 2.8K 
[   ]ci1.2bit30-Jun-2004 15:12 29M 
[   ]ci1.chrom.sizes28-Feb-2012 16:11 47K 
[TXT]md5sum.txt05-May-2014 16:14 290  

Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80