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 -
chainSusScr2Link.txt.gz 2010-05-16 11:47 12G
chainOviAri1Link.txt.gz 2011-04-25 07:49 4.3G
chainSusScr2.txt.gz 2010-05-16 11:07 3.0G
chainOviAri1.txt.gz 2011-04-25 08:52 2.3G
chainHg19Link.txt.gz 2009-09-20 07:36 968M
chainCanFam2Link.txt.gz 2008-04-07 12:48 670M
chainMm9Link.txt.gz 2008-04-07 14:35 497M
xenoMrna.txt.gz 2016-02-21 10:04 309M
chainOrnAna1Link.txt.gz 2008-04-07 14:58 249M
chainHg19.txt.gz 2009-09-20 07:33 234M
rmsk.txt.gz 2008-04-07 15:43 135M
multiz5way.txt.gz 2008-04-07 15:19 91M
netOviAri1.txt.gz 2011-04-25 07:31 80M
chainCanFam2.txt.gz 2008-04-07 12:17 74M
netCanFam2.txt.gz 2008-04-07 15:25 73M
netSusScr2.txt.gz 2010-05-16 11:22 73M
phastCons5way.txt.gz 2008-04-07 15:34 70M
netHg19.txt.gz 2009-09-20 07:41 68M
chainMm9.txt.gz 2008-04-07 14:19 64M
all_est.txt.gz 2016-06-05 09:04 64M
quality.txt.gz 2008-04-07 15:39 58M
netMm9.txt.gz 2008-04-07 15:15 56M
chainOrnAna1.txt.gz 2008-04-07 14:50 45M
intronEst.txt.gz 2016-06-05 09:03 37M
xenoRefGene.txt.gz 2020-08-20 21:48 32M
xenoRefSeqAli.txt.gz 2020-08-20 21:48 31M
xenoRefFlat.txt.gz 2020-08-20 21:48 29M
estOrientInfo.txt.gz 2016-06-05 09:04 20M
netOrnAna1.txt.gz 2008-04-07 15:31 18M
nestedRepeats.txt.gz 2008-04-07 15:22 15M
simpleRepeat.txt.gz 2008-04-07 15:46 12M
gc5Base.txt.gz 2008-04-07 15:10 11M
genscanPep.txt.gz 2010-10-31 13:25 11M
phastConsElements5way.txt.gz 2008-04-07 15:36 9.8M
multiz5waySummary.txt.gz 2008-04-07 15:21 9.8M
multiz5wayFrames.txt.gz 2008-04-07 15:21 7.7M
ensPep.txt.gz 2011-03-14 08:25 7.3M
nscanPep.txt.gz 2008-04-25 03:16 5.1M
blastHg18KG.txt.gz 2009-12-20 10:21 4.0M
genscan.txt.gz 2008-04-07 15:10 3.2M
ensGene.txt.gz 2011-03-14 08:23 2.4M
augustusGene.txt.gz 2015-07-26 10:13 2.3M
gold.txt.gz 2008-04-07 15:10 2.3M
all_mrna.txt.gz 2020-08-20 21:48 1.6M
refSeqAli.txt.gz 2020-08-20 21:48 1.5M
refGene.txt.gz 2020-08-20 21:48 1.5M
nscanGene.txt.gz 2008-04-25 03:16 1.4M
refFlat.txt.gz 2020-08-20 21:48 1.4M
gap.txt.gz 2008-04-07 15:04 1.0M
mgcFullMrna.txt.gz 2020-03-01 04:52 908K
cpgIslandExtUnmasked.txt.gz 2014-06-01 08:32 889K
cpgIslandExt.txt.gz 2008-04-07 15:04 805K
mgcGenes.txt.gz 2020-03-01 04:52 803K
mrnaOrientInfo.txt.gz 2020-08-20 21:48 591K
ensGtp.txt.gz 2011-03-14 08:23 323K
microsat.txt.gz 2015-08-23 10:14 299K
ensemblToGeneName.txt.gz 2011-10-03 07:42 199K
ensemblSource.txt.gz 2011-10-03 07:42 119K
tRNAs.txt.gz 2012-04-22 18:28 109K
chromInfo.txt.gz 2008-04-07 15:04 60K
cytoBandIdeo.txt.gz 2013-08-11 03:45 56K
trackDb.txt.gz 2023-03-28 13:46 50K
trackDb_pushedout.txt.gz 2021-12-27 12:21 49K
gbLoaded.txt.gz 2020-08-20 21:54 43K
wgEncodeNhgriBip.txt.gz 2009-08-02 05:56 11K
tableDescriptions.txt.gz 2024-04-27 02:03 6.8K
tableList.txt.gz 2024-04-28 03:23 4.3K
netHg19.sql 2009-09-20 07:41 2.3K
blastHg18KG.sql 2009-12-20 10:21 2.3K
netOrnAna1.sql 2008-04-07 15:30 2.2K
netCanFam2.sql 2008-04-07 15:22 2.2K
netMm9.sql 2008-04-07 15:12 2.2K
xenoRefSeqAli.sql 2020-08-20 21:48 2.1K
refSeqAli.sql 2020-08-20 21:48 2.1K
all_mrna.sql 2020-08-20 21:48 2.1K
mgcFullMrna.sql 2020-03-01 04:52 2.1K
intronEst.sql 2016-06-05 09:03 2.1K
xenoMrna.sql 2016-02-21 10:02 2.1K
all_est.sql 2016-06-05 09:04 2.1K
trackDb_pushedout.sql 2021-12-27 12:21 2.1K
trackDb.sql 2023-03-28 13:46 2.1K
netSusScr2.sql 2010-05-16 11:22 2.0K
netOviAri1.sql 2011-04-25 07:31 2.0K
xenoRefGene.sql 2020-08-20 21:48 2.0K
refGene.sql 2020-08-20 21:48 1.9K
augustusGene.sql 2015-07-26 10:13 1.9K
mgcGenes.sql 2020-03-01 04:52 1.9K
simpleRepeat.sql 2008-04-07 15:46 1.9K
nestedRepeats.sql 2008-04-07 15:21 1.9K
nscanGene.sql 2008-04-25 03:16 1.9K
rmsk.sql 2008-04-07 15:40 1.9K
ensGene.sql 2011-03-14 08:23 1.9K
mrnaOrientInfo.sql 2020-08-20 21:48 1.8K
hgFindSpec_pushedout.sql 2021-12-27 12:21 1.8K
chainHg19.sql 2009-09-20 07:33 1.8K
estOrientInfo.sql 2016-06-05 09:04 1.8K
hgFindSpec.sql 2023-03-28 13:46 1.8K
xenoRefFlat.sql 2020-08-20 21:48 1.7K
phastCons5way.sql 2008-04-07 15:31 1.7K
refFlat.sql 2020-08-20 21:48 1.7K
quality.sql 2008-04-07 15:36 1.7K
gc5Base.sql 2008-04-07 15:09 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 08:32 1.7K
wgEncodeNhgriBip.sql 2009-08-02 05:56 1.7K
tRNAs.sql 2012-04-22 18:28 1.7K
multiz5wayFrames.sql 2008-04-07 15:21 1.7K
chainOrnAna1.sql 2008-04-07 14:49 1.7K
chainCanFam2.sql 2008-04-07 12:14 1.7K
chainSusScr2.sql 2010-05-16 11:01 1.6K
chainOviAri1.sql 2011-04-25 08:41 1.6K
chainMm9.sql 2008-04-07 14:17 1.6K
cpgIslandExt.sql 2008-04-07 15:04 1.6K
gbLoaded.sql 2020-08-20 21:54 1.6K
gold.sql 2008-04-07 15:10 1.6K
tableList.sql 2024-04-28 03:23 1.6K
genscan.sql 2008-04-07 15:10 1.6K
chainHg19Link.sql 2009-09-20 07:34 1.5K
cytoBandIdeo.sql 2013-08-11 03:45 1.5K
gap.sql 2008-04-07 15:04 1.5K
microsat.sql 2015-08-23 10:14 1.5K
chainSusScr2Link.sql 2010-05-16 11:22 1.5K
chainOviAri1Link.sql 2011-04-25 07:32 1.5K
multiz5waySummary.sql 2008-04-07 15:21 1.5K
tableDescriptions.sql 2024-04-27 02:03 1.5K
phastConsElements5way.sql 2008-04-07 15:36 1.4K
history.sql 2008-04-07 15:10 1.4K
chainOrnAna1Link.sql 2008-04-07 14:51 1.4K
chainCanFam2Link.sql 2008-04-07 12:20 1.4K
multiz5way.sql 2008-04-07 15:16 1.4K
chainMm9Link.sql 2008-04-07 14:20 1.4K
bigFiles.sql 2024-04-28 03:23 1.4K
grp.sql 2014-03-02 03:37 1.4K
ensGtp.sql 2011-03-14 08:23 1.4K
ensemblToGeneName.sql 2011-10-03 07:42 1.3K
ensemblSource.sql 2011-10-03 07:42 1.3K
genscanPep.sql 2010-10-31 13:25 1.3K
extFile.sql 2008-04-07 14:51 1.3K
ensPep.sql 2011-03-14 08:25 1.3K
chromInfo.sql 2008-04-07 15:04 1.2K
nscanPep.sql 2008-04-25 03:16 1.1K
hgFindSpec.txt.gz 2023-03-28 13:46 1.0K
hgFindSpec_pushedout.txt.gz 2021-12-27 12:21 961
history.txt.gz 2008-04-07 15:10 742
grp.txt.gz 2014-03-02 03:37 208
extFile.txt.gz 2008-04-07 14:51 85
bigFiles.txt.gz 2024-04-28 03:23 33