This directory contains the May 2005 assembly of the rabbit genome 
(oryCun1) obtained from the Broad Institute. More information may be 
found at http://www.broad.mit.edu/mammals/.

Files included in this directory:
assembly.agp.gz - Description of how the assembly was generated from
     fragments.  

oryCun1.quals.fa.gz - quality scores in fasta file format

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

rmsk.out.gz - RepeatMasker .out file for scaffolds. These were created 
    by RepeatMasker at the -s sensitive setting. 

scaffold.fa.gz - unmasked scaffolds sequences obtained from the Broad
    Institute.

scaffoldSoftMask.fa.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.  RepeatMasker May 3 2005 (open-3-1-0) version with RepBase 
    libraries: RepBase Update 9.11, RM database version 20050112.

trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, and translated into one 
    .bed file for all the scaffolds.  


oryCun1.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/oryCun1/bigZips. To download multiple files, 
use the "mget" command:

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

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      md5sum.txt              2009-06-10 10:24  301   
      oryCun1.chrom.sizes     2005-05-22 10:16  4.3M  
      trf.bed.gz              2005-05-22 08:12  5.7M  
      assembly.agp.gz         2005-05-20 18:05   15M  
      rmsk.out.gz             2005-05-22 08:01  100M  
      scaffold.fa.gz          2005-05-21 10:15  642M  
      scaffoldSoftMask.fa.gz  2005-05-22 08:21  683M  
      oryCun1.quals.fa.gz     2009-06-09 09:58  860M