This directory contains sequence for C. elegans version WS120
deposited into Wormbase as of 1 March 2004. The sequence may also
be downloaded from WormBase at
ftp://ftp.sanger.ac.uk/pub/wormbase/FROZEN_RELEASES/WS120/CHROMOSOMES/.

Files included in this directory:

ce2.2bit - contains the complete C. elegans/ce2 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 assembly was generated,
     unpacking to one file per chromosome.  

chromFa.zip - 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
    files contain clones that are not yet finished or cannot be placed
    with certainty at a specific place on the chromosome. In some
    cases, including the human HLA region on chromosome 6, the
    chrN_random.fa files also contain haplotypes that differ from the
    main assembly.

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

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

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

est.fa.gz - C. elegans 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. elegans 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.

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts for RefSeq genes with annotated 5' UTRs.  
    This file is updated weekly so it could be slightly out 
    of sync with the RefSeq data which is updated daily for most 
    assemblies.

upstream2000.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - Same as upstream1000, but 5000 bases.

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 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/ce2/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. elegans 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.