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 - xenoRefSeqAli.txt.gz 2020-08-21 01:34 31M xenoRefSeqAli.sql 2020-08-21 01:34 2.1K xenoRefGene.txt.gz 2020-08-21 01:34 30M xenoRefGene.sql 2020-08-21 01:34 2.0K xenoRefFlat.txt.gz 2020-08-21 01:34 28M xenoRefFlat.sql 2020-08-21 01:34 1.7K xenoMrna.txt.gz 2020-08-21 00:52 270M xenoMrna.sql 2020-08-21 00:52 2.1K windowmaskerSdust.txt.gz 2012-06-20 14:52 124M windowmaskerSdust.sql 2012-06-20 14:52 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:41 28K ucscToRefSeq.sql 2018-02-18 05:41 1.4K ucscToINSDC.txt.gz 2013-09-15 09:50 27K ucscToINSDC.sql 2013-09-15 09:50 1.4K trackDb.txt.gz 2024-07-25 09:34 82K trackDb.sql 2024-07-25 09:34 2.1K tableList.txt.gz 2024-12-01 03:32 4.4K tableList.sql 2024-12-01 03:32 1.6K tableDescriptions.txt.gz 2024-11-30 02:03 7.0K tableDescriptions.sql 2024-11-30 02:03 1.5K simpleRepeat.txt.gz 2012-06-20 14:42 23M simpleRepeat.sql 2012-06-20 14:42 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.2M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K rmsk.txt.gz 2012-06-20 14:40 121M rmsk.sql 2012-06-20 14:39 1.8K refSeqAli.txt.gz 2020-08-21 01:34 187K refSeqAli.sql 2020-08-21 01:34 2.1K refGene.txt.gz 2020-08-21 01:34 182K refGene.sql 2020-08-21 01:34 1.9K refFlat.txt.gz 2020-08-21 01:34 170K refFlat.sql 2020-08-21 01:34 1.7K oregannoLink.txt.gz 2016-05-15 07:58 450K oregannoLink.sql 2016-05-15 07:58 1.4K oregannoAttr.txt.gz 2016-05-15 07:58 365K oregannoAttr.sql 2016-05-15 07:58 1.4K oreganno.txt.gz 2016-05-15 07:58 426K oreganno.sql 2016-05-15 07:58 1.5K netXenTro9.txt.gz 2017-12-14 09:10 5.8M netXenTro9.sql 2017-12-14 09:10 2.1K netTarSyr2.txt.gz 2015-05-24 21:40 74M netTarSyr2.sql 2015-05-24 21:40 2.1K netRn6.txt.gz 2017-03-26 16:52 59M netRn6.sql 2017-03-26 16:50 2.1K netMm10.txt.gz 2012-06-20 14:41 59M netMm10.sql 2012-06-20 14:41 2.0K netHg38.txt.gz 2015-05-17 20:36 64M netHg38.sql 2015-05-17 20:36 2.1K netHg19.txt.gz 2013-02-03 11:35 64M netHg19.sql 2013-02-03 11:35 2.1K netFelCat8.txt.gz 2016-01-12 13:31 53M netFelCat8.sql 2016-01-12 13:31 2.1K netCanFam4.txt.gz 2020-05-13 01:06 3.4M netCanFam4.sql 2020-05-13 01:06 2.1K nestedRepeats.txt.gz 2012-06-20 14:39 14M nestedRepeats.sql 2012-06-20 14:39 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.8M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 12M ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.1M ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 177K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 401K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:26 4.0M ncbiRefSeq.sql 2020-05-10 03:26 1.9K mrnaOrientInfo.txt.gz 2020-08-21 01:34 91K mrnaOrientInfo.sql 2020-08-21 01:34 1.8K microsat.txt.gz 2015-08-23 11:48 629K microsat.sql 2015-08-23 11:48 1.5K intronEst.txt.gz 2016-06-12 06:24 9.2M intronEst.sql 2016-06-12 06:24 2.1K history.txt.gz 2012-06-20 14:42 409 history.sql 2012-06-20 14:42 1.5K hgFindSpec.txt.gz 2024-07-25 09:34 1.3K hgFindSpec.sql 2024-07-25 09:34 1.8K grp.txt.gz 2014-03-02 03:40 208 grp.sql 2014-03-02 03:40 1.3K gold.txt.gz 2012-06-20 14:39 105K gold.sql 2012-06-20 14:39 1.6K genscanSubopt.txt.gz 2012-06-20 14:29 5.3M genscanSubopt.sql 2012-06-20 14:29 1.5K genscan.txt.gz 2012-06-20 14:42 3.0M genscan.sql 2012-06-20 14:42 1.6K geneid.txt.gz 2015-11-22 13:35 2.1M geneid.sql 2015-11-22 13:35 1.9K gc5BaseBw.txt.gz 2012-06-20 14:38 63 gc5BaseBw.sql 2012-06-20 14:38 1.2K gbLoaded.txt.gz 2020-08-21 01:34 92K gbLoaded.sql 2020-08-21 01:34 1.6K gap.txt.gz 2012-06-20 14:42 330K gap.sql 2012-06-20 14:42 1.5K extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 extNcbiRefSeq.sql 2020-05-10 03:26 1.4K estOrientInfo.txt.gz 2016-06-12 06:28 4.4M estOrientInfo.sql 2016-06-12 06:28 1.8K ensemblToGeneName.txt.gz 2021-05-25 14:22 269K ensemblToGeneName.sql 2021-05-25 14:22 1.4K ensemblSource.txt.gz 2021-05-25 14:23 186K ensemblSource.sql 2021-05-25 14:23 1.4K ensPep.txt.gz 2021-05-25 14:24 16M ensPep.sql 2021-05-25 14:24 1.3K ensGtp.txt.gz 2021-05-25 14:22 599K ensGtp.sql 2021-05-25 14:22 1.4K ensGene.txt.gz 2021-05-25 14:22 3.4M ensGene.sql 2021-05-25 14:22 1.9K cytoBandIdeo.txt.gz 2013-04-28 11:34 18K cytoBandIdeo.sql 2013-04-28 11:34 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 09:45 1.1M cpgIslandExtUnmasked.sql 2014-06-01 09:45 1.7K cpgIslandExt.txt.gz 2012-06-20 15:18 1.0M cpgIslandExt.sql 2012-06-20 15:18 1.6K chromInfo.txt.gz 2012-06-20 14:39 19K chromInfo.sql 2012-06-20 14:39 1.3K chromAlias.txt.gz 2018-02-18 05:41 34K chromAlias.sql 2018-02-18 05:41 1.4K chainXenTro9Link.txt.gz 2017-12-14 09:10 181M chainXenTro9Link.sql 2017-12-14 09:10 1.5K chainXenTro9.txt.gz 2017-12-14 09:09 46M chainXenTro9.sql 2017-12-14 09:09 1.7K chainTarSyr2Link.txt.gz 2015-05-24 21:36 1.1G chainTarSyr2Link.sql 2015-05-24 21:35 1.5K chainTarSyr2.txt.gz 2015-05-24 21:34 298M chainTarSyr2.sql 2015-05-24 21:34 1.7K chainRn6Link.txt.gz 2017-03-26 16:33 488M chainRn6Link.sql 2017-03-26 16:28 1.5K chainRn6.txt.gz 2017-03-26 16:25 60M chainRn6.sql 2017-03-26 16:25 1.7K chainMm10Link.txt.gz 2012-06-20 14:44 455M chainMm10Link.sql 2012-06-20 14:43 1.5K chainMm10.txt.gz 2012-06-20 14:19 56M chainMm10.sql 2012-06-20 14:18 1.6K chainHg38Link.txt.gz 2015-05-17 20:39 857M chainHg38Link.sql 2015-05-17 20:38 1.5K chainHg38.txt.gz 2015-05-17 20:35 188M chainHg38.sql 2015-05-17 20:35 1.7K chainHg19Link.txt.gz 2013-02-03 11:32 823M chainHg19Link.sql 2013-02-03 11:30 1.5K chainHg19.txt.gz 2013-02-03 11:30 181M chainHg19.sql 2013-02-03 11:29 1.7K chainFelCat8Link.txt.gz 2016-01-12 13:28 659M chainFelCat8Link.sql 2016-01-12 13:27 1.5K chainFelCat8.txt.gz 2016-01-12 13:27 106M chainFelCat8.sql 2016-01-12 13:27 1.7K chainCanFam4Link.txt.gz 2020-05-13 01:05 6.4G chainCanFam4Link.sql 2020-05-13 01:05 1.6K chainCanFam4.txt.gz 2020-05-12 23:53 740M chainCanFam4.sql 2020-05-12 23:53 1.7K bigFiles.txt.gz 2024-12-01 03:32 94 bigFiles.sql 2024-12-01 03:32 1.4K augustusGene.txt.gz 2015-07-26 11:04 2.3M augustusGene.sql 2015-07-26 11:03 1.9K all_mrna.txt.gz 2020-08-21 00:52 233K all_mrna.sql 2020-08-21 00:52 2.1K all_est.txt.gz 2016-06-12 06:24 17M all_est.sql 2016-06-12 06:24 2.1K