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