This directory contains a dump of the UCSC genome annotation database for the
    Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) assembly of the dog genome
    (canFam4, Uppsala University) .

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    https://www.ncbi.nlm.nih.gov/genome/85
    https://www.ncbi.nlm.nih.gov/genome/assembly/6119491
    https://www.ncbi.nlm.nih.gov/bioproject/587469
    https://www.ncbi.nlm.nih.gov/biosample/SAMN13230619

Files included in this directory (updated nightly):

  - *.sql files:  the MySQL commands used to create the tables

  - *.txt.gz files: the database tables in a tab-delimited format
    compressed with gzip.

To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
  http://genome.ucsc.edu/cgi-bin/hgTables?db=canFam4
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

---------------------------------------------------------------
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.soe.ucsc.edu, then go to
the directory goldenPath/canFam4/database/. 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/canFam4/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

To uncompress the *.txt.gz files:
    gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.

To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql canFam4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql canFam4 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - gap.sql 31-Mar-2020 10:33 1.6K gap.txt.gz 31-Mar-2020 10:33 7.2K gold.sql 31-Mar-2020 10:33 1.7K gold.txt.gz 31-Mar-2020 10:33 37K cpgIslandExtUnmasked.sql 31-Mar-2020 10:56 1.7K cpgIslandExtUnmasked.txt.gz 31-Mar-2020 10:56 1.1M cytoBandIdeo.sql 31-Mar-2020 11:00 1.5K cytoBandIdeo.txt.gz 31-Mar-2020 11:00 13K gc5BaseBw.sql 31-Mar-2020 11:00 1.3K gc5BaseBw.txt.gz 31-Mar-2020 11:00 66 grp.sql 31-Mar-2020 11:00 1.3K grp.txt.gz 31-Mar-2020 11:00 213 chromInfo.sql 31-Mar-2020 11:02 1.4K chromInfo.txt.gz 31-Mar-2020 11:02 14K simpleRepeat.sql 31-Mar-2020 12:19 1.9K simpleRepeat.txt.gz 31-Mar-2020 12:19 27M microsat.sql 31-Mar-2020 15:38 1.5K microsat.txt.gz 31-Mar-2020 15:38 672K rmsk.sql 31-Mar-2020 15:40 1.9K rmsk.txt.gz 31-Mar-2020 15:40 128M nestedRepeats.sql 31-Mar-2020 15:42 1.9K nestedRepeats.txt.gz 31-Mar-2020 15:42 15M windowmaskerSdust.sql 31-Mar-2020 17:05 1.5K windowmaskerSdust.txt.gz 31-Mar-2020 17:05 125M cpgIslandExt.sql 02-Apr-2020 09:50 1.7K cpgIslandExt.txt.gz 02-Apr-2020 09:50 1.0M ucscToINSDC.sql 02-Apr-2020 11:42 1.4K ucscToINSDC.txt.gz 02-Apr-2020 11:42 19K chainMm10.sql 09-Apr-2020 15:40 1.7K chainMm10.txt.gz 09-Apr-2020 15:40 58M chainMm10Link.sql 09-Apr-2020 15:43 1.5K chainMm10Link.txt.gz 09-Apr-2020 15:43 474M netMm10.sql 09-Apr-2020 15:51 2.1K netMm10.txt.gz 09-Apr-2020 15:51 60M genscan.sql 09-Apr-2020 15:57 1.7K genscan.txt.gz 09-Apr-2020 15:57 3.1M chainHg38.sql 09-Apr-2020 16:05 1.7K chainHg38.txt.gz 09-Apr-2020 16:05 408M chainHg38Link.sql 09-Apr-2020 16:17 1.5K chainHg38Link.txt.gz 09-Apr-2020 16:17 1.2G netHg38.sql 09-Apr-2020 16:25 2.1K netHg38.txt.gz 09-Apr-2020 16:25 66M augustusGene.sql 10-Apr-2020 10:30 1.9K augustusGene.txt.gz 10-Apr-2020 10:30 2.3M crisprAllTargets.sql 16-Apr-2020 02:07 1.3K crisprAllTargets.txt.gz 16-Apr-2020 02:07 69 all_mrna.sql 05-May-2020 20:49 2.1K all_mrna.txt.gz 05-May-2020 20:49 224K xenoMrna.sql 05-May-2020 20:50 2.1K xenoMrna.txt.gz 05-May-2020 20:50 223M refFlat.sql 05-May-2020 21:19 1.7K refFlat.txt.gz 05-May-2020 21:19 169K refGene.sql 05-May-2020 21:19 1.9K refGene.txt.gz 05-May-2020 21:19 182K xenoRefGene.sql 05-May-2020 21:19 1.9K xenoRefGene.txt.gz 05-May-2020 21:19 12M refSeqAli.sql 05-May-2020 21:19 2.1K refSeqAli.txt.gz 05-May-2020 21:19 189K xenoRefFlat.sql 05-May-2020 21:19 1.7K xenoRefFlat.txt.gz 05-May-2020 21:19 11M xenoRefSeqAli.sql 05-May-2020 21:19 2.1K xenoRefSeqAli.txt.gz 05-May-2020 21:19 22M all_est.sql 06-May-2020 00:36 2.1K all_est.txt.gz 06-May-2020 00:36 17M estOrientInfo.sql 06-May-2020 00:36 1.8K estOrientInfo.txt.gz 06-May-2020 00:36 4.5M intronEst.sql 06-May-2020 00:36 2.1K intronEst.txt.gz 06-May-2020 00:36 8.9M gbLoaded.sql 06-May-2020 00:55 1.6K gbLoaded.txt.gz 06-May-2020 00:55 1.4K mrnaOrientInfo.sql 06-May-2020 00:55 1.8K mrnaOrientInfo.txt.gz 06-May-2020 00:55 88K chainCanFam3.sql 13-May-2020 09:53 1.7K chainCanFam3.txt.gz 13-May-2020 09:53 734M chainCanFam3Link.sql 13-May-2020 10:59 1.5K chainCanFam3Link.txt.gz 13-May-2020 10:59 6.4G netCanFam3.sql 13-May-2020 11:07 2.1K netCanFam3.txt.gz 13-May-2020 11:07 5.6M chromAlias.sql 20-May-2020 10:44 1.4K chromAlias.txt.gz 20-May-2020 10:44 12K history.sql 20-May-2020 11:32 1.6K history.txt.gz 20-May-2020 11:32 815 chainNeoSch1.sql 13-Jul-2020 22:45 1.7K chainNeoSch1.txt.gz 13-Jul-2020 22:45 408M chainNeoSch1Link.sql 13-Jul-2020 23:03 1.5K chainNeoSch1Link.txt.gz 13-Jul-2020 23:03 1.9G netNeoSch1.sql 13-Jul-2020 23:11 2.1K netNeoSch1.txt.gz 13-Jul-2020 23:11 56M tableDescriptions.sql 07-Nov-2020 02:03 1.4K tableDescriptions.txt.gz 07-Nov-2020 02:03 5.3K hgFindSpec.sql 19-Nov-2020 16:21 1.7K hgFindSpec.txt.gz 19-Nov-2020 16:21 633 trackDb.sql 19-Nov-2020 16:21 2.0K trackDb.txt.gz 19-Nov-2020 16:21 35K tableList.sql 22-Nov-2020 03:16 1.5K tableList.txt.gz 22-Nov-2020 03:16 2.9K bigFiles.sql 22-Nov-2020 03:16 1.4K bigFiles.txt.gz 22-Nov-2020 03:16 95