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;'
------------------------------------------------------------------
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 -
chainMm10.sql 2012-06-20 14:18 1.6K
chainMm10.txt.gz 2012-06-20 14:19 56M
genscanSubopt.sql 2012-06-20 14:29 1.5K
genscanSubopt.txt.gz 2012-06-20 14:29 5.3M
gc5BaseBw.sql 2012-06-20 14:38 1.2K
gc5BaseBw.txt.gz 2012-06-20 14:38 63
nestedRepeats.sql 2012-06-20 14:39 1.9K
nestedRepeats.txt.gz 2012-06-20 14:39 14M
gold.sql 2012-06-20 14:39 1.6K
gold.txt.gz 2012-06-20 14:39 105K
chromInfo.sql 2012-06-20 14:39 1.3K
chromInfo.txt.gz 2012-06-20 14:39 19K
rmsk.sql 2012-06-20 14:39 1.8K
rmsk.txt.gz 2012-06-20 14:40 121M
netMm10.sql 2012-06-20 14:41 2.0K
netMm10.txt.gz 2012-06-20 14:41 59M
gap.sql 2012-06-20 14:42 1.5K
gap.txt.gz 2012-06-20 14:42 330K
genscan.sql 2012-06-20 14:42 1.6K
genscan.txt.gz 2012-06-20 14:42 3.0M
history.sql 2012-06-20 14:42 1.5K
history.txt.gz 2012-06-20 14:42 409
simpleRepeat.sql 2012-06-20 14:42 1.9K
simpleRepeat.txt.gz 2012-06-20 14:42 23M
chainMm10Link.sql 2012-06-20 14:43 1.5K
chainMm10Link.txt.gz 2012-06-20 14:44 455M
windowmaskerSdust.sql 2012-06-20 14:52 1.4K
windowmaskerSdust.txt.gz 2012-06-20 14:52 124M
cpgIslandExt.sql 2012-06-20 15:18 1.6K
cpgIslandExt.txt.gz 2012-06-20 15:18 1.0M
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
netHg19.sql 2013-02-03 11:35 2.1K
netHg19.txt.gz 2013-02-03 11:35 64M
cytoBandIdeo.sql 2013-04-28 11:34 1.5K
cytoBandIdeo.txt.gz 2013-04-28 11:34 18K
ucscToINSDC.sql 2013-09-15 09:50 1.4K
ucscToINSDC.txt.gz 2013-09-15 09:50 27K
grp.sql 2014-03-02 03:40 1.3K
grp.txt.gz 2014-03-02 03:40 208
cpgIslandExtUnmasked.sql 2014-06-01 09:45 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 09:45 1.1M
chainHg38.sql 2015-05-17 20:35 1.7K
chainHg38.txt.gz 2015-05-17 20:35 188M
netHg38.sql 2015-05-17 20:36 2.1K
netHg38.txt.gz 2015-05-17 20:36 64M
chainHg38Link.sql 2015-05-17 20:38 1.5K
chainHg38Link.txt.gz 2015-05-17 20:39 857M
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
netTarSyr2.sql 2015-05-24 21:40 2.1K
netTarSyr2.txt.gz 2015-05-24 21:40 74M
augustusGene.sql 2015-07-26 11:03 1.9K
augustusGene.txt.gz 2015-07-26 11:04 2.3M
microsat.sql 2015-08-23 11:48 1.5K
microsat.txt.gz 2015-08-23 11:48 629K
geneid.sql 2015-11-22 13:35 1.9K
geneid.txt.gz 2015-11-22 13:35 2.1M
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
netFelCat8.sql 2016-01-12 13:31 2.1K
netFelCat8.txt.gz 2016-01-12 13:31 53M
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
all_est.sql 2016-06-12 06:24 2.1K
all_est.txt.gz 2016-06-12 06:24 17M
intronEst.sql 2016-06-12 06:24 2.1K
intronEst.txt.gz 2016-06-12 06:24 9.2M
estOrientInfo.sql 2016-06-12 06:28 1.8K
estOrientInfo.txt.gz 2016-06-12 06:28 4.4M
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
netRn6.sql 2017-03-26 16:50 2.1K
netRn6.txt.gz 2017-03-26 16:52 59M
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
netXenTro9.sql 2017-12-14 09:10 2.1K
netXenTro9.txt.gz 2017-12-14 09:10 5.8M
chromAlias.sql 2018-02-18 05:41 1.4K
chromAlias.txt.gz 2018-02-18 05:41 34K
ucscToRefSeq.sql 2018-02-18 05:41 1.4K
ucscToRefSeq.txt.gz 2018-02-18 05:41 28K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
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
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.2M
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 1.6K
chainCanFam4Link.txt.gz 2020-05-13 01:05 6.4G
netCanFam4.sql 2020-05-13 01:06 2.1K
netCanFam4.txt.gz 2020-05-13 01:06 3.4M
all_mrna.sql 2020-08-21 00:52 2.1K
all_mrna.txt.gz 2020-08-21 00:52 233K
xenoMrna.sql 2020-08-21 00:52 2.1K
xenoMrna.txt.gz 2020-08-21 00:52 270M
refGene.sql 2020-08-21 01:34 1.9K
refGene.txt.gz 2020-08-21 01:34 182K
refFlat.sql 2020-08-21 01:34 1.7K
refFlat.txt.gz 2020-08-21 01:34 170K
xenoRefGene.sql 2020-08-21 01:34 2.0K
xenoRefGene.txt.gz 2020-08-21 01:34 30M
xenoRefFlat.sql 2020-08-21 01:34 1.7K
xenoRefFlat.txt.gz 2020-08-21 01:34 28M
mrnaOrientInfo.sql 2020-08-21 01:34 1.8K
mrnaOrientInfo.txt.gz 2020-08-21 01:34 91K
refSeqAli.sql 2020-08-21 01:34 2.1K
refSeqAli.txt.gz 2020-08-21 01:34 187K
xenoRefSeqAli.sql 2020-08-21 01:34 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 01:34 31M
gbLoaded.sql 2020-08-21 01:34 1.6K
gbLoaded.txt.gz 2020-08-21 01:34 92K
ensGene.sql 2021-05-25 14:22 1.9K
ensGene.txt.gz 2021-05-25 14:22 3.4M
ensGtp.sql 2021-05-25 14:22 1.4K
ensGtp.txt.gz 2021-05-25 14:22 599K
ensemblToGeneName.sql 2021-05-25 14:22 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:22 269K
ensemblSource.sql 2021-05-25 14:23 1.4K
ensemblSource.txt.gz 2021-05-25 14:23 186K
ensPep.sql 2021-05-25 14:24 1.3K
ensPep.txt.gz 2021-05-25 14:24 16M
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 82K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 7.0K
tableList.sql 2024-11-17 03:37 1.6K
tableList.txt.gz 2024-11-17 03:37 4.4K
bigFiles.sql 2024-11-17 03:37 1.4K
bigFiles.txt.gz 2024-11-17 03:37 94