This directory contains the Dec. 2011 (Baylor/dasNov3) assembly of the armadillo genome
(dasNov3, Baylor College of Medicine Dasnov3.0 (GCA_000208655.2)), as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/235
    http://www.ncbi.nlm.nih.gov/genome/assembly/326198
    http://www.ncbi.nlm.nih.gov/bioproject/12594

Files included in this directory:

dasNov3.2bit - contains the complete armadillo/dasNov3 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

dasNov3.agp.gz - Description of how the assembly was generated from
    fragments.

dasNov3.fa.gz - "Soft-masked" assembly sequence in one file.
    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.

dasNov3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

dasNov3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    April 26 2011 (open-3-3-0) version of RepeatMasker
    RepBase library: RELEASE 20110920

dasNov3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format.

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Armadillo 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.

dasNov3.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

dasNov3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
dasNov3.gc5Base.wig.gz - wiggle database table for the GC Percent track
                    - this is an older standard alternative to the current
                    - bigWig format of the track, sometimes usefull for analysis
dasNov3.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:  http://genome.ucsc.edu/goldenPath/help/wiggle.html
    and  http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

dasNov3.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

------------------------------------------------------------------
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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/dasNov3/bigZips. To download multiple files, use
the "mget" command:

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

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/dasNov3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/dasNov3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/dasNov3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/dasNov3/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

For conditions of use regarding the Armadillo genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use

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GenBank Data Usage

The GenBank database is designed to provide and encourage access within 
the scientific community to the most up to date and comprehensive DNA 
sequence information. Therefore, NCBI places no restrictions on the use 
or distribution of the GenBank data. However, some submitters may claim 
patent, copyright, or other intellectual property rights in all or a 
portion of the data they have submitted. NCBI is not in a position to 
assess the validity of such claims, and therefore cannot provide comment 
or unrestricted permission concerning the use, copying, or distribution 
of the information contained in GenBank.
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      Name                          Last modified      Size  Description
Parent Directory - xenoMrna.fa.gz 2020-02-27 04:37 6.8G dasNov3.gc5Base.wigVarStep.gz 2012-04-11 10:52 1.6G dasNov3.fa.gz 2012-07-13 12:26 1.0G dasNov3.2bit 2012-04-13 10:48 902M dasNov3.gc5Base.wib 2019-01-17 14:47 659M dasNov3.fa.masked.gz 2012-07-13 12:38 560M xenoRefMrna.fa.gz 2020-02-27 04:38 337M dasNov3.fa.out.gz 2012-07-13 12:10 161M dasNov3.gc5Base.wig.gz 2019-01-17 14:47 15M dasNov3.agp.gz 2012-07-13 12:08 7.4M dasNov3.trf.bed.gz 2012-07-13 12:10 3.4M dasNov3.chromAlias.txt 2020-09-29 10:48 1.7M dasNov3.chrom.sizes 2012-04-11 10:40 737K mrna.fa.gz 2020-02-27 04:28 13K md5sum.txt 2019-01-17 15:53 479 xenoRefMrna.fa.gz.md5 2020-02-27 04:38 52 xenoMrna.fa.gz.md5 2020-02-27 04:38 49 mrna.fa.gz.md5 2020-02-27 04:28 45 genes/ 2020-10-02 13:37 -