This directory contains a dump of the UCSC genome annotation database for
the Oct. 2007 assembly of the cow genome (bosTau4, Baylor Release 4.0).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Baylor College of Medicine Human Genome Sequencing Center.
For more information on the cow genome, see the project website:
<A HREF="http://www.hgsc.bcm.tmc.edu/projects/bovine/"
TARGET=_blank>Baylor College of Medicine Human Genome Sequencing Center</A>
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=bosTau4
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/bosTau4/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/bosTau4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/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 bosTau4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau4 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
For conditions of use regarding the Cow genome sequence data, see
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html .
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
all_est.sql 05-Jun-2016 09:04 2.1K
all_est.txt.gz 05-Jun-2016 09:04 64M
all_mrna.sql 09-Jul-2017 07:34 2.1K
all_mrna.txt.gz 09-Jul-2017 07:34 1.6M
augustusGene.sql 26-Jul-2015 10:13 1.9K
augustusGene.txt.gz 26-Jul-2015 10:13 2.3M
bigFiles.sql 09-Jul-2017 07:34 1.4K
bigFiles.txt.gz 09-Jul-2017 07:34 33
blastHg18KG.sql 20-Dec-2009 10:21 2.3K
blastHg18KG.txt.gz 20-Dec-2009 10:21 4.0M
chainCanFam2.sql 07-Apr-2008 12:14 1.7K
chainCanFam2.txt.gz 07-Apr-2008 12:17 74M
chainCanFam2Link.sql 07-Apr-2008 12:20 1.4K
chainCanFam2Link.txt.gz 07-Apr-2008 12:48 670M
chainHg19.sql 20-Sep-2009 07:33 1.8K
chainHg19.txt.gz 20-Sep-2009 07:33 234M
chainHg19Link.sql 20-Sep-2009 07:34 1.5K
chainHg19Link.txt.gz 20-Sep-2009 07:36 968M
chainMm9.sql 07-Apr-2008 14:17 1.6K
chainMm9.txt.gz 07-Apr-2008 14:19 64M
chainMm9Link.sql 07-Apr-2008 14:20 1.4K
chainMm9Link.txt.gz 07-Apr-2008 14:35 497M
chainOrnAna1.sql 07-Apr-2008 14:49 1.7K
chainOrnAna1.txt.gz 07-Apr-2008 14:50 45M
chainOrnAna1Link.sql 07-Apr-2008 14:51 1.4K
chainOrnAna1Link.txt.gz 07-Apr-2008 14:58 249M
chainOviAri1.sql 25-Apr-2011 08:41 1.6K
chainOviAri1.txt.gz 25-Apr-2011 08:52 2.3G
chainOviAri1Link.sql 25-Apr-2011 07:32 1.5K
chainOviAri1Link.txt.gz 25-Apr-2011 07:49 4.3G
chainSusScr2.sql 16-May-2010 11:01 1.6K
chainSusScr2.txt.gz 16-May-2010 11:07 3.0G
chainSusScr2Link.sql 16-May-2010 11:22 1.5K
chainSusScr2Link.txt.gz 16-May-2010 11:47 12G
chromInfo.sql 07-Apr-2008 15:04 1.2K
chromInfo.txt.gz 07-Apr-2008 15:04 60K
cpgIslandExt.sql 07-Apr-2008 15:04 1.6K
cpgIslandExt.txt.gz 07-Apr-2008 15:04 805K
cpgIslandExtUnmasked.sql 01-Jun-2014 08:32 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 08:32 889K
cytoBandIdeo.sql 11-Aug-2013 03:45 1.5K
cytoBandIdeo.txt.gz 11-Aug-2013 03:45 56K
ensGene.sql 14-Mar-2011 08:23 1.9K
ensGene.txt.gz 14-Mar-2011 08:23 2.4M
ensGtp.sql 14-Mar-2011 08:23 1.4K
ensGtp.txt.gz 14-Mar-2011 08:23 323K
ensPep.sql 14-Mar-2011 08:25 1.3K
ensPep.txt.gz 14-Mar-2011 08:25 7.3M
ensemblSource.sql 03-Oct-2011 07:42 1.3K
ensemblSource.txt.gz 03-Oct-2011 07:42 119K
ensemblToGeneName.sql 03-Oct-2011 07:42 1.3K
ensemblToGeneName.txt.gz 03-Oct-2011 07:42 199K
estOrientInfo.sql 05-Jun-2016 09:04 1.8K
estOrientInfo.txt.gz 05-Jun-2016 09:04 20M
extFile.sql 07-Apr-2008 14:51 1.3K
extFile.txt.gz 07-Apr-2008 14:51 85
gap.sql 07-Apr-2008 15:04 1.5K
gap.txt.gz 07-Apr-2008 15:04 1.0M
gbLoaded.sql 09-Jul-2017 07:34 1.6K
gbLoaded.txt.gz 09-Jul-2017 07:34 16K
gc5Base.sql 07-Apr-2008 15:09 1.7K
gc5Base.txt.gz 07-Apr-2008 15:10 11M
genscan.sql 07-Apr-2008 15:10 1.6K
genscan.txt.gz 07-Apr-2008 15:10 3.2M
genscanPep.sql 31-Oct-2010 13:25 1.3K
genscanPep.txt.gz 31-Oct-2010 13:25 11M
gold.sql 07-Apr-2008 15:10 1.6K
gold.txt.gz 07-Apr-2008 15:10 2.3M
grp.sql 02-Mar-2014 03:37 1.4K
grp.txt.gz 02-Mar-2014 03:37 208
hgFindSpec.sql 09-Jul-2017 07:34 1.7K
hgFindSpec.txt.gz 09-Jul-2017 07:34 972
history.sql 07-Apr-2008 15:10 1.4K
history.txt.gz 07-Apr-2008 15:10 742
intronEst.sql 05-Jun-2016 09:03 2.1K
intronEst.txt.gz 05-Jun-2016 09:03 37M
mgcFullMrna.sql 05-Jun-2016 09:04 2.1K
mgcFullMrna.txt.gz 05-Jun-2016 09:04 930K
mgcGenes.sql 05-Jun-2016 09:03 1.9K
mgcGenes.txt.gz 05-Jun-2016 09:03 888K
microsat.sql 23-Aug-2015 10:14 1.5K
microsat.txt.gz 23-Aug-2015 10:14 299K
mrnaOrientInfo.sql 09-Jul-2017 07:35 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 07:35 579K
multiz5way.sql 07-Apr-2008 15:16 1.4K
multiz5way.txt.gz 07-Apr-2008 15:19 91M
multiz5wayFrames.sql 07-Apr-2008 15:21 1.7K
multiz5wayFrames.txt.gz 07-Apr-2008 15:21 7.7M
multiz5waySummary.sql 07-Apr-2008 15:21 1.5K
multiz5waySummary.txt.gz 07-Apr-2008 15:21 9.8M
nestedRepeats.sql 07-Apr-2008 15:21 1.9K
nestedRepeats.txt.gz 07-Apr-2008 15:22 15M
netCanFam2.sql 07-Apr-2008 15:22 2.2K
netCanFam2.txt.gz 07-Apr-2008 15:25 73M
netHg19.sql 20-Sep-2009 07:41 2.3K
netHg19.txt.gz 20-Sep-2009 07:41 68M
netMm9.sql 07-Apr-2008 15:12 2.2K
netMm9.txt.gz 07-Apr-2008 15:15 56M
netOrnAna1.sql 07-Apr-2008 15:30 2.2K
netOrnAna1.txt.gz 07-Apr-2008 15:31 18M
netOviAri1.sql 25-Apr-2011 07:31 2.0K
netOviAri1.txt.gz 25-Apr-2011 07:31 80M
netSusScr2.sql 16-May-2010 11:22 2.0K
netSusScr2.txt.gz 16-May-2010 11:22 73M
nscanGene.sql 25-Apr-2008 03:16 1.9K
nscanGene.txt.gz 25-Apr-2008 03:16 1.4M
nscanPep.sql 25-Apr-2008 03:16 1.1K
nscanPep.txt.gz 25-Apr-2008 03:16 5.1M
phastCons5way.sql 07-Apr-2008 15:31 1.7K
phastCons5way.txt.gz 07-Apr-2008 15:34 70M
phastConsElements5way.sql 07-Apr-2008 15:36 1.4K
phastConsElements5way.txt.gz 07-Apr-2008 15:36 9.8M
quality.sql 07-Apr-2008 15:36 1.7K
quality.txt.gz 07-Apr-2008 15:39 58M
refFlat.sql 09-Jul-2017 07:35 1.7K
refFlat.txt.gz 09-Jul-2017 07:35 1.4M
refGene.sql 09-Jul-2017 07:34 1.9K
refGene.txt.gz 09-Jul-2017 07:34 1.5M
refSeqAli.sql 09-Jul-2017 07:34 2.1K
refSeqAli.txt.gz 09-Jul-2017 07:34 1.5M
rmsk.sql 07-Apr-2008 15:40 1.9K
rmsk.txt.gz 07-Apr-2008 15:43 135M
simpleRepeat.sql 07-Apr-2008 15:46 1.9K
simpleRepeat.txt.gz 07-Apr-2008 15:46 12M
tRNAs.sql 22-Apr-2012 18:28 1.7K
tRNAs.txt.gz 22-Apr-2012 18:28 109K
tableDescriptions.sql 09-Jul-2017 07:34 1.4K
tableDescriptions.txt.gz 09-Jul-2017 07:34 5.9K
tableList.sql 09-Jul-2017 07:34 1.5K
tableList.txt.gz 09-Jul-2017 07:34 4.1K
trackDb.sql 09-Jul-2017 07:34 2.0K
trackDb.txt.gz 09-Jul-2017 07:34 44K
wgEncodeNhgriBip.sql 02-Aug-2009 05:56 1.7K
wgEncodeNhgriBip.txt.gz 02-Aug-2009 05:56 11K
xenoMrna.sql 21-Feb-2016 10:02 2.1K
xenoMrna.txt.gz 21-Feb-2016 10:04 309M
xenoRefFlat.sql 09-Jul-2017 07:35 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 07:35 25M
xenoRefGene.sql 09-Jul-2017 07:34 1.9K
xenoRefGene.txt.gz 09-Jul-2017 07:34 27M
xenoRefSeqAli.sql 09-Jul-2017 07:34 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 07:34 24M