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