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;'

-----------------------------------------------------------------------------
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 2020-03-31 11:00 66 crisprAllTargets.txt.gz 2020-04-16 02:07 69 ncbiRefSeqOther.txt.gz 2022-01-26 15:08 75 extNcbiRefSeq.txt.gz 2022-01-26 15:08 91 altAllele.txt.gz 2020-09-08 16:34 112 bigFiles.txt.gz 2022-08-14 03:04 175 grp.txt.gz 2020-03-31 11:00 213 history.txt.gz 2020-05-20 11:32 815 hgFindSpec.txt.gz 2022-05-04 11:41 1.0K gc5BaseBw.sql 2020-03-31 11:00 1.3K altAllele.sql 2020-09-08 16:34 1.3K crisprAllTargets.sql 2020-04-16 02:07 1.3K ncbiRefSeqOther.sql 2022-01-26 15:08 1.3K grp.sql 2020-03-31 11:00 1.3K ncbiRefSeqCds.sql 2022-01-26 15:08 1.4K bigFiles.sql 2022-08-14 03:04 1.4K ncbiRefSeqPepTable.sql 2022-01-26 15:08 1.4K chromInfo.sql 2020-03-31 11:02 1.4K gbLoaded.txt.gz 2020-05-06 00:55 1.4K chromAlias.sql 2020-05-20 10:44 1.4K tableDescriptions.sql 2022-05-04 06:34 1.4K ucscToINSDC.sql 2020-04-02 11:42 1.4K extNcbiRefSeq.sql 2022-01-26 15:08 1.5K microsat.sql 2020-03-31 15:38 1.5K structVar.sql 2020-09-08 15:26 1.5K windowmaskerSdust.sql 2020-03-31 17:05 1.5K cytoBandIdeo.sql 2020-03-31 11:00 1.5K chainHg38Link.sql 2020-04-09 16:17 1.5K chainMm10Link.sql 2020-04-09 15:43 1.5K chainCanFam3Link.sql 2020-05-13 10:59 1.5K chainNeoSch1Link.sql 2020-07-13 23:03 1.5K tableList.sql 2022-08-14 03:04 1.6K seqNcbiRefSeq.sql 2022-01-26 15:08 1.6K history.sql 2020-05-20 11:32 1.6K gbLoaded.sql 2020-05-06 00:55 1.6K gap.sql 2020-03-31 10:33 1.6K gold.sql 2020-03-31 10:33 1.7K genscan.sql 2020-04-09 15:57 1.7K cpgIslandExt.sql 2020-04-02 09:50 1.7K miRNA.sql 2020-09-09 16:31 1.7K chainHg38.sql 2020-04-09 16:05 1.7K chainMm10.sql 2020-04-09 15:40 1.7K refFlat.sql 2020-05-05 21:19 1.7K chainCanFam3.sql 2020-05-13 09:53 1.7K chainNeoSch1.sql 2020-07-13 22:45 1.7K cpgIslandExtUnmasked.sql 2020-03-31 10:56 1.7K xenoRefFlat.sql 2020-05-05 21:19 1.7K hgFindSpec.sql 2022-05-04 11:41 1.8K estOrientInfo.sql 2020-05-06 00:36 1.8K mrnaOrientInfo.sql 2020-05-06 00:55 1.8K uuGene.sql 2020-09-08 15:09 1.8K rmsk.sql 2020-03-31 15:40 1.9K refGene.sql 2020-05-05 21:19 1.9K simpleRepeat.sql 2020-03-31 12:19 1.9K nestedRepeats.sql 2020-03-31 15:42 1.9K xenoRefGene.sql 2020-05-05 21:19 1.9K augustusGene.sql 2020-04-10 10:30 1.9K ncbiRefSeq.sql 2022-01-26 15:04 2.0K ncbiRefSeqCurated.sql 2022-01-26 15:04 2.0K ncbiRefSeqPredicted.sql 2022-01-26 15:04 2.0K ncbiRefSeqLink.sql 2022-01-26 15:04 2.0K trackDb.sql 2022-05-04 11:41 2.1K netHg38.sql 2020-04-09 16:25 2.1K netMm10.sql 2020-04-09 15:51 2.1K netCanFam3.sql 2020-05-13 11:07 2.1K netNeoSch1.sql 2020-07-13 23:11 2.1K all_est.sql 2020-05-06 00:36 2.1K all_mrna.sql 2020-05-05 20:49 2.1K xenoMrna.sql 2020-05-05 20:50 2.1K intronEst.sql 2020-05-06 00:36 2.1K refSeqAli.sql 2020-05-05 21:19 2.1K xenoRefSeqAli.sql 2020-05-05 21:19 2.1K ncbiRefSeqPsl.sql 2022-01-26 15:04 2.1K tableList.txt.gz 2022-08-14 03:04 3.6K tableDescriptions.txt.gz 2022-05-04 06:34 6.4K gap.txt.gz 2020-03-31 10:33 7.2K chromAlias.txt.gz 2020-05-20 10:44 12K cytoBandIdeo.txt.gz 2020-03-31 11:00 13K chromInfo.txt.gz 2020-03-31 11:02 14K miRNA.txt.gz 2020-09-09 16:31 18K ucscToINSDC.txt.gz 2020-04-02 11:42 19K trackDb.txt.gz 2022-05-04 11:41 34K gold.txt.gz 2020-03-31 10:33 37K mrnaOrientInfo.txt.gz 2020-05-06 00:55 88K refFlat.txt.gz 2020-05-05 21:19 169K refGene.txt.gz 2020-05-05 21:19 182K refSeqAli.txt.gz 2020-05-05 21:19 189K ncbiRefSeqCurated.txt.gz 2022-01-26 15:04 190K all_mrna.txt.gz 2020-05-05 20:49 224K ncbiRefSeqCds.txt.gz 2022-01-26 15:08 427K microsat.txt.gz 2020-03-31 15:38 672K cpgIslandExt.txt.gz 2020-04-02 09:50 1.0M cpgIslandExtUnmasked.txt.gz 2020-03-31 10:56 1.1M seqNcbiRefSeq.txt.gz 2022-01-26 15:08 1.4M structVar.txt.gz 2020-09-08 15:26 1.8M ncbiRefSeqLink.txt.gz 2022-01-26 15:04 2.1M augustusGene.txt.gz 2020-04-10 10:30 2.3M genscan.txt.gz 2020-04-09 15:57 3.1M ncbiRefSeqPredicted.txt.gz 2022-01-26 15:04 4.1M ncbiRefSeq.txt.gz 2022-01-26 15:04 4.3M estOrientInfo.txt.gz 2020-05-06 00:36 4.5M netCanFam3.txt.gz 2020-05-13 11:07 5.6M ncbiRefSeqPsl.txt.gz 2022-01-26 15:04 6.1M ncbiRefSeqPepTable.txt.gz 2022-01-26 15:08 7.4M uuGene.txt.gz 2020-09-08 15:09 8.4M intronEst.txt.gz 2020-05-06 00:36 8.9M xenoRefFlat.txt.gz 2020-05-05 21:19 11M xenoRefGene.txt.gz 2020-05-05 21:19 12M nestedRepeats.txt.gz 2020-03-31 15:42 15M all_est.txt.gz 2020-05-06 00:36 17M xenoRefSeqAli.txt.gz 2020-05-05 21:19 22M simpleRepeat.txt.gz 2020-03-31 12:19 27M netNeoSch1.txt.gz 2020-07-13 23:11 56M chainMm10.txt.gz 2020-04-09 15:40 58M netMm10.txt.gz 2020-04-09 15:51 60M netHg38.txt.gz 2020-04-09 16:25 66M windowmaskerSdust.txt.gz 2020-03-31 17:05 125M rmsk.txt.gz 2020-03-31 15:40 128M xenoMrna.txt.gz 2020-05-05 20:50 223M chainNeoSch1.txt.gz 2020-07-13 22:45 408M chainHg38.txt.gz 2020-04-09 16:05 408M chainMm10Link.txt.gz 2020-04-09 15:43 474M chainCanFam3.txt.gz 2020-05-13 09:53 734M chainHg38Link.txt.gz 2020-04-09 16:17 1.2G chainNeoSch1Link.txt.gz 2020-07-13 23:03 1.9G chainCanFam3Link.txt.gz 2020-05-13 10:59 6.4G