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