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 12-Jun-2016 06:24 2.1K
all_est.txt.gz 12-Jun-2016 06:24 17M
all_mrna.sql 13-Jun-2017 16:03 2.1K
all_mrna.txt.gz 13-Jun-2017 16:03 222K
augustusGene.sql 26-Jul-2015 11:03 1.9K
augustusGene.txt.gz 26-Jul-2015 11:04 2.3M
bigFiles.sql 09-Jul-2017 08:03 1.4K
bigFiles.txt.gz 09-Jul-2017 08:03 68
chainFelCat8.sql 12-Jan-2016 13:27 1.7K
chainFelCat8.txt.gz 12-Jan-2016 13:27 106M
chainFelCat8Link.sql 12-Jan-2016 13:27 1.5K
chainFelCat8Link.txt.gz 12-Jan-2016 13:28 659M
chainHg19.sql 03-Feb-2013 11:29 1.7K
chainHg19.txt.gz 03-Feb-2013 11:30 181M
chainHg19Link.sql 03-Feb-2013 11:30 1.5K
chainHg19Link.txt.gz 03-Feb-2013 11:32 823M
chainHg38.sql 17-May-2015 20:35 1.7K
chainHg38.txt.gz 17-May-2015 20:35 188M
chainHg38Link.sql 17-May-2015 20:38 1.5K
chainHg38Link.txt.gz 17-May-2015 20:39 857M
chainMm10.sql 20-Jun-2012 14:18 1.6K
chainMm10.txt.gz 20-Jun-2012 14:19 56M
chainMm10Link.sql 20-Jun-2012 14:43 1.5K
chainMm10Link.txt.gz 20-Jun-2012 14:44 455M
chainRn6.sql 26-Mar-2017 16:25 1.7K
chainRn6.txt.gz 26-Mar-2017 16:25 60M
chainRn6Link.sql 26-Mar-2017 16:28 1.5K
chainRn6Link.txt.gz 26-Mar-2017 16:33 488M
chainTarSyr2.sql 24-May-2015 21:34 1.7K
chainTarSyr2.txt.gz 24-May-2015 21:34 298M
chainTarSyr2Link.sql 24-May-2015 21:35 1.5K
chainTarSyr2Link.txt.gz 24-May-2015 21:36 1.1G
chromInfo.sql 20-Jun-2012 14:39 1.3K
chromInfo.txt.gz 20-Jun-2012 14:39 19K
cpgIslandExt.sql 20-Jun-2012 15:18 1.6K
cpgIslandExt.txt.gz 20-Jun-2012 15:18 1.0M
cpgIslandExtUnmasked.sql 01-Jun-2014 09:45 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 09:45 1.1M
cytoBandIdeo.sql 28-Apr-2013 11:34 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 11:34 18K
ensGene.sql 20-Nov-2016 06:05 1.9K
ensGene.txt.gz 20-Nov-2016 06:05 2.7M
ensGtp.sql 20-Nov-2016 06:04 1.4K
ensGtp.txt.gz 20-Nov-2016 06:04 387K
ensPep.sql 20-Nov-2016 06:04 1.3K
ensPep.txt.gz 20-Nov-2016 06:04 7.9M
ensemblSource.sql 20-Nov-2016 06:05 1.4K
ensemblSource.txt.gz 20-Nov-2016 06:05 122K
ensemblToGeneName.sql 20-Nov-2016 06:09 1.4K
ensemblToGeneName.txt.gz 20-Nov-2016 06:09 148K
estOrientInfo.sql 12-Jun-2016 06:28 1.8K
estOrientInfo.txt.gz 12-Jun-2016 06:28 4.4M
gap.sql 20-Jun-2012 14:42 1.5K
gap.txt.gz 20-Jun-2012 14:42 330K
gbLoaded.sql 09-Jul-2017 08:02 1.6K
gbLoaded.txt.gz 09-Jul-2017 08:02 64K
gc5BaseBw.sql 20-Jun-2012 14:38 1.2K
gc5BaseBw.txt.gz 20-Jun-2012 14:38 63
geneid.sql 22-Nov-2015 13:35 1.9K
geneid.txt.gz 22-Nov-2015 13:35 2.1M
genscan.sql 20-Jun-2012 14:42 1.6K
genscan.txt.gz 20-Jun-2012 14:42 3.0M
genscanSubopt.sql 20-Jun-2012 14:29 1.5K
genscanSubopt.txt.gz 20-Jun-2012 14:29 5.3M
gold.sql 20-Jun-2012 14:39 1.6K
gold.txt.gz 20-Jun-2012 14:39 105K
grp.sql 02-Mar-2014 03:40 1.3K
grp.txt.gz 02-Mar-2014 03:40 208
hgFindSpec.sql 09-Jul-2017 08:06 1.7K
hgFindSpec.txt.gz 09-Jul-2017 08:06 809
history.sql 20-Jun-2012 14:42 1.5K
history.txt.gz 20-Jun-2012 14:42 409
intronEst.sql 12-Jun-2016 06:24 2.1K
intronEst.txt.gz 12-Jun-2016 06:24 9.2M
microsat.sql 23-Aug-2015 11:48 1.5K
microsat.txt.gz 23-Aug-2015 11:48 629K
mrnaOrientInfo.sql 09-Jul-2017 08:06 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 08:06 88K
nestedRepeats.sql 20-Jun-2012 14:39 1.9K
nestedRepeats.txt.gz 20-Jun-2012 14:39 14M
netFelCat8.sql 12-Jan-2016 13:31 2.1K
netFelCat8.txt.gz 12-Jan-2016 13:31 53M
netHg19.sql 03-Feb-2013 11:35 2.1K
netHg19.txt.gz 03-Feb-2013 11:35 64M
netHg38.sql 17-May-2015 20:36 2.1K
netHg38.txt.gz 17-May-2015 20:36 64M
netMm10.sql 20-Jun-2012 14:41 2.0K
netMm10.txt.gz 20-Jun-2012 14:41 59M
netRn6.sql 26-Mar-2017 16:50 2.1K
netRn6.txt.gz 26-Mar-2017 16:52 59M
netTarSyr2.sql 24-May-2015 21:40 2.1K
netTarSyr2.txt.gz 24-May-2015 21:40 74M
oreganno.sql 15-May-2016 07:58 1.5K
oreganno.txt.gz 15-May-2016 07:58 426K
oregannoAttr.sql 15-May-2016 07:58 1.4K
oregannoAttr.txt.gz 15-May-2016 07:58 365K
oregannoLink.sql 15-May-2016 07:58 1.4K
oregannoLink.txt.gz 15-May-2016 07:58 450K
refFlat.sql 09-Jul-2017 08:06 1.7K
refFlat.txt.gz 09-Jul-2017 08:06 170K
refGene.sql 09-Jul-2017 08:02 1.9K
refGene.txt.gz 09-Jul-2017 08:02 182K
refSeqAli.sql 09-Jul-2017 08:02 2.1K
refSeqAli.txt.gz 09-Jul-2017 08:02 185K
rmsk.sql 20-Jun-2012 14:39 1.8K
rmsk.txt.gz 20-Jun-2012 14:40 121M
simpleRepeat.sql 20-Jun-2012 14:42 1.9K
simpleRepeat.txt.gz 20-Jun-2012 14:42 23M
tableDescriptions.sql 09-Jul-2017 08:03 1.4K
tableDescriptions.txt.gz 09-Jul-2017 08:03 4.9K
tableList.sql 09-Jul-2017 08:02 1.5K
tableList.txt.gz 09-Jul-2017 08:02 3.5K
trackDb.sql 09-Jul-2017 08:06 2.0K
trackDb.txt.gz 09-Jul-2017 08:06 35K
ucscToINSDC.sql 15-Sep-2013 09:50 1.4K
ucscToINSDC.txt.gz 15-Sep-2013 09:50 27K
windowmaskerSdust.sql 20-Jun-2012 14:52 1.4K
windowmaskerSdust.txt.gz 20-Jun-2012 14:52 124M
xenoMrna.sql 09-Jul-2017 08:03 2.1K
xenoMrna.txt.gz 09-Jul-2017 08:05 242M
xenoRefFlat.sql 09-Jul-2017 08:02 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 08:03 25M
xenoRefGene.sql 09-Jul-2017 08:02 1.9K
xenoRefGene.txt.gz 09-Jul-2017 08:02 27M
xenoRefSeqAli.sql 09-Jul-2017 08:03 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 08:03 26M