This directory contains a dump of the UCSC genome annotation database for
the Sep. 2011 (Broad CanFam3.1/canFam3) assembly of the dog genome
(canFam3, Broad CanFam3.1 (GCA_000002285.2)).
The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/85
    http://www.ncbi.nlm.nih.gov/genome/assembly/317138
    http://www.ncbi.nlm.nih.gov/bioproject/13179

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=canFam3
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.cse.ucsc.edu, then go to 
the directory goldenPath/canFam3/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.cse.ucsc.edu/goldenPath/canFam3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/canFam3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/database/gc5BaseBw.txt.gz' 
        -O gc5BaseBw.txt.gz

Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/

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 canFam3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql canFam3 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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

The dog genome sequence is made freely available by the Dog Genome Sequencing
Project. Please cite the following publication when using these data:

Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype
structure of the domestic dog. Nature. 2005 Dec 8;438:803-19.
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      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2016-06-12 06:24 2.1K all_est.txt.gz 2016-06-12 06:24 17M all_mrna.sql 2020-08-21 00:52 2.1K all_mrna.txt.gz 2020-08-21 00:52 233K augustusGene.sql 2015-07-26 11:03 1.9K augustusGene.txt.gz 2015-07-26 11:04 2.3M bigFiles.sql 2021-05-02 03:12 1.4K bigFiles.txt.gz 2021-05-02 03:12 94 chainCanFam4.sql 2020-05-12 23:53 1.7K chainCanFam4.txt.gz 2020-05-12 23:53 740M chainCanFam4Link.sql 2020-05-13 01:05 1.5K chainCanFam4Link.txt.gz 2020-05-13 01:05 6.4G chainFelCat8.sql 2016-01-12 13:27 1.7K chainFelCat8.txt.gz 2016-01-12 13:27 106M chainFelCat8Link.sql 2016-01-12 13:27 1.5K chainFelCat8Link.txt.gz 2016-01-12 13:28 659M chainHg19.sql 2013-02-03 11:29 1.7K chainHg19.txt.gz 2013-02-03 11:30 181M chainHg19Link.sql 2013-02-03 11:30 1.5K chainHg19Link.txt.gz 2013-02-03 11:32 823M chainHg38.sql 2015-05-17 20:35 1.7K chainHg38.txt.gz 2015-05-17 20:35 188M chainHg38Link.sql 2015-05-17 20:38 1.5K chainHg38Link.txt.gz 2015-05-17 20:39 857M chainMm10.sql 2012-06-20 14:18 1.6K chainMm10.txt.gz 2012-06-20 14:19 56M chainMm10Link.sql 2012-06-20 14:43 1.5K chainMm10Link.txt.gz 2012-06-20 14:44 455M chainRn6.sql 2017-03-26 16:25 1.7K chainRn6.txt.gz 2017-03-26 16:25 60M chainRn6Link.sql 2017-03-26 16:28 1.5K chainRn6Link.txt.gz 2017-03-26 16:33 488M chainTarSyr2.sql 2015-05-24 21:34 1.7K chainTarSyr2.txt.gz 2015-05-24 21:34 298M chainTarSyr2Link.sql 2015-05-24 21:35 1.5K chainTarSyr2Link.txt.gz 2015-05-24 21:36 1.1G chainXenTro9.sql 2017-12-14 09:09 1.7K chainXenTro9.txt.gz 2017-12-14 09:09 46M chainXenTro9Link.sql 2017-12-14 09:10 1.5K chainXenTro9Link.txt.gz 2017-12-14 09:10 181M chromAlias.sql 2018-02-18 05:41 1.4K chromAlias.txt.gz 2018-02-18 05:41 34K chromInfo.sql 2012-06-20 14:39 1.3K chromInfo.txt.gz 2012-06-20 14:39 19K cpgIslandExt.sql 2012-06-20 15:18 1.6K cpgIslandExt.txt.gz 2012-06-20 15:18 1.0M cpgIslandExtUnmasked.sql 2014-06-01 09:45 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 09:45 1.1M cytoBandIdeo.sql 2013-04-28 11:34 1.5K cytoBandIdeo.txt.gz 2013-04-28 11:34 18K ensGene.sql 2020-08-31 15:20 1.9K ensGene.txt.gz 2020-08-31 15:20 3.4M ensGtp.sql 2020-08-31 15:20 1.4K ensGtp.txt.gz 2020-08-31 15:20 594K ensPep.sql 2020-08-31 15:43 1.3K ensPep.txt.gz 2020-08-31 15:43 16M ensemblSource.sql 2020-08-31 15:43 1.4K ensemblSource.txt.gz 2020-08-31 15:43 186K ensemblToGeneName.sql 2020-08-31 15:20 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:20 273K estOrientInfo.sql 2016-06-12 06:28 1.8K estOrientInfo.txt.gz 2016-06-12 06:28 4.4M extNcbiRefSeq.sql 2020-05-10 03:26 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 gap.sql 2012-06-20 14:42 1.5K gap.txt.gz 2012-06-20 14:42 330K gbLoaded.sql 2020-08-21 01:34 1.6K gbLoaded.txt.gz 2020-08-21 01:34 92K gc5BaseBw.sql 2012-06-20 14:38 1.2K gc5BaseBw.txt.gz 2012-06-20 14:38 63 geneid.sql 2015-11-22 13:35 1.9K geneid.txt.gz 2015-11-22 13:35 2.1M genscan.sql 2012-06-20 14:42 1.6K genscan.txt.gz 2012-06-20 14:42 3.0M genscanSubopt.sql 2012-06-20 14:29 1.5K genscanSubopt.txt.gz 2012-06-20 14:29 5.3M gold.sql 2012-06-20 14:39 1.6K gold.txt.gz 2012-06-20 14:39 105K grp.sql 2014-03-02 03:40 1.3K grp.txt.gz 2014-03-02 03:40 208 hgFindSpec.sql 2020-10-25 07:45 1.7K hgFindSpec.txt.gz 2020-10-25 07:45 1.3K history.sql 2012-06-20 14:42 1.5K history.txt.gz 2012-06-20 14:42 409 intronEst.sql 2016-06-12 06:24 2.1K intronEst.txt.gz 2016-06-12 06:24 9.2M microsat.sql 2015-08-23 11:48 1.5K microsat.txt.gz 2015-08-23 11:48 629K mrnaOrientInfo.sql 2020-08-21 01:34 1.8K mrnaOrientInfo.txt.gz 2020-08-21 01:34 91K ncbiRefSeq.sql 2020-05-10 03:26 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:26 4.0M ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 401K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 177K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.1M ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 12M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.8M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M nestedRepeats.sql 2012-06-20 14:39 1.9K nestedRepeats.txt.gz 2012-06-20 14:39 14M netCanFam4.sql 2020-05-13 01:06 2.1K netCanFam4.txt.gz 2020-05-13 01:06 3.4M netFelCat8.sql 2016-01-12 13:31 2.1K netFelCat8.txt.gz 2016-01-12 13:31 53M netHg19.sql 2013-02-03 11:35 2.1K netHg19.txt.gz 2013-02-03 11:35 64M netHg38.sql 2015-05-17 20:36 2.1K netHg38.txt.gz 2015-05-17 20:36 64M netMm10.sql 2012-06-20 14:41 2.0K netMm10.txt.gz 2012-06-20 14:41 59M netRn6.sql 2017-03-26 16:50 2.1K netRn6.txt.gz 2017-03-26 16:52 59M netTarSyr2.sql 2015-05-24 21:40 2.1K netTarSyr2.txt.gz 2015-05-24 21:40 74M netXenTro9.sql 2017-12-14 09:10 2.1K netXenTro9.txt.gz 2017-12-14 09:10 5.8M oreganno.sql 2016-05-15 07:58 1.5K oreganno.txt.gz 2016-05-15 07:58 426K oregannoAttr.sql 2016-05-15 07:58 1.4K oregannoAttr.txt.gz 2016-05-15 07:58 365K oregannoLink.sql 2016-05-15 07:58 1.4K oregannoLink.txt.gz 2016-05-15 07:58 450K refFlat.sql 2020-08-21 01:34 1.7K refFlat.txt.gz 2020-08-21 01:34 170K refGene.sql 2020-08-21 01:34 1.9K refGene.txt.gz 2020-08-21 01:34 182K refSeqAli.sql 2020-08-21 01:34 2.1K refSeqAli.txt.gz 2020-08-21 01:34 187K rmsk.sql 2012-06-20 14:39 1.8K rmsk.txt.gz 2012-06-20 14:40 121M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.2M simpleRepeat.sql 2012-06-20 14:42 1.9K simpleRepeat.txt.gz 2012-06-20 14:42 23M tableDescriptions.sql 2020-07-04 02:04 1.4K tableDescriptions.txt.gz 2020-07-04 02:04 7.0K tableList.sql 2021-05-02 03:12 1.6K tableList.txt.gz 2021-05-02 03:12 4.4K trackDb.sql 2020-10-22 20:34 2.0K trackDb.txt.gz 2020-10-22 20:34 48K ucscToINSDC.sql 2013-09-15 09:50 1.4K ucscToINSDC.txt.gz 2013-09-15 09:50 27K ucscToRefSeq.sql 2018-02-18 05:41 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:41 28K windowmaskerSdust.sql 2012-06-20 14:52 1.4K windowmaskerSdust.txt.gz 2012-06-20 14:52 124M xenoMrna.sql 2020-08-21 00:52 2.1K xenoMrna.txt.gz 2020-08-21 00:52 270M xenoRefFlat.sql 2020-08-21 01:34 1.7K xenoRefFlat.txt.gz 2020-08-21 01:34 28M xenoRefGene.sql 2020-08-21 01:34 1.9K xenoRefGene.txt.gz 2020-08-21 01:34 30M xenoRefSeqAli.sql 2020-08-21 01:34 2.1K xenoRefSeqAli.txt.gz 2020-08-21 01:34 31M