This directory contains the Nov. 2017 (Felis_catus_9.0/felCat9) assembly of the
    cat genome (felCat9, Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine),
    as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:
    https://www.ncbi.nlm.nih.gov/genome/78
    https://www.ncbi.nlm.nih.gov/genome/assembly/1448961
    https://www.ncbi.nlm.nih.gov/bioproject/16726
    https://www.ncbi.nlm.nih.gov/bioproject/SAMN02953640

Files included in this directory:

felCat9.2bit - contains the complete cat/felCat9 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.soe.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
	http://genome.ucsc.edu/admin/jk-install.html

felCat9.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

felCat9.agp.gz - Description of how the assembly was generated from
    fragments.

felCat9.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.

felCat9.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

felCat9.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    January 31 2015 (open-4-0-5) version of RepeatMasker
    RepBase library: RELEASE 20140131

felCat9.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.

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

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Cat 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 of RefSeq genes with annotated 5' UTRs.
    This file is updated weekly so it might 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.
felCat9.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
felCat9.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
felCat9.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

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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.soe.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/felCat9/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.soe.ucsc.edu/goldenPath/felCat9/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/felCat9/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat9/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat9/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

The Cat sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases.

2. Users are free to use the data in scientific papers analyzing these data
   if the providers of these data are properly acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. The centers producing the data reserve the right to publish the initial
   large-scale analyses of the data set, including large-scale identification
   of regions of evolutionary conservation and large-scale genomic assembly.
   Large-scale refers to regions with size on the order of a chromosome (that
   is, 30 Mb or more).

4. Any redistribution of the data should carry this notice.

-----------------------------------------------------------------------------
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 - felCat9.chrom.sizes 27-Feb-2018 13:16 119K felCat9.gc5Base.wigVarStep.gz 27-Feb-2018 13:32 1.2G felCat9.2bit 28-Feb-2018 10:39 631M felCat9.agp.gz 19-Mar-2018 10:23 66K felCat9.fa.out.gz 19-Mar-2018 10:24 153M felCat9.trf.bed.gz 19-Mar-2018 10:24 10M felCat9.fa.gz 19-Mar-2018 10:37 774M felCat9.fa.masked.gz 19-Mar-2018 10:46 463M upstream1000.fa.gz 19-Mar-2018 10:46 74K upstream2000.fa.gz 19-Mar-2018 10:46 141K upstream5000.fa.gz 19-Mar-2018 10:46 339K felCat9.gc5Base.wib 17-Jan-2019 14:48 472M felCat9.gc5Base.wig.gz 17-Jan-2019 14:48 9.1M md5sum.txt 17-Jan-2019 15:54 692 mrna.fa.gz 15-Oct-2019 18:37 1.0M mrna.fa.gz.md5 15-Oct-2019 18:37 45 xenoMrna.fa.gz 15-Oct-2019 18:47 6.8G xenoMrna.fa.gz.md5 15-Oct-2019 18:47 49 est.fa.gz 15-Oct-2019 18:51 177K est.fa.gz.md5 15-Oct-2019 18:51 44 xenoRefMrna.fa.gz 15-Oct-2019 18:52 331M xenoRefMrna.fa.gz.md5 15-Oct-2019 18:52 52 refMrna.fa.gz 15-Oct-2019 18:52 236K refMrna.fa.gz.md5 15-Oct-2019 18:52 48 genes/ 27-Apr-2020 14:08 -