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 -
xenoRefSeqAli.txt.gz 2020-08-20 21:48 31M
xenoRefSeqAli.sql 2020-08-20 21:48 2.1K
xenoRefGene.txt.gz 2020-08-20 21:48 32M
xenoRefGene.sql 2020-08-20 21:48 2.0K
xenoRefFlat.txt.gz 2020-08-20 21:48 29M
xenoRefFlat.sql 2020-08-20 21:48 1.7K
xenoMrna.txt.gz 2016-02-21 10:04 309M
xenoMrna.sql 2016-02-21 10:02 2.1K
wgEncodeNhgriBip.txt.gz 2009-08-02 05:56 11K
wgEncodeNhgriBip.sql 2009-08-02 05:56 1.7K
trackDb.txt.gz 2023-03-28 13:46 50K
trackDb.sql 2023-03-28 13:46 2.1K
tableList.txt.gz 2024-11-24 03:20 4.2K
tableList.sql 2024-11-24 03:20 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 6.8K
tableDescriptions.sql 2024-11-23 02:03 1.4K
tRNAs.txt.gz 2012-04-22 18:28 109K
tRNAs.sql 2012-04-22 18:28 1.7K
simpleRepeat.txt.gz 2008-04-07 15:46 12M
simpleRepeat.sql 2008-04-07 15:46 1.9K
rmsk.txt.gz 2008-04-07 15:43 135M
rmsk.sql 2008-04-07 15:40 1.9K
refSeqAli.txt.gz 2020-08-20 21:48 1.5M
refSeqAli.sql 2020-08-20 21:48 2.1K
refGene.txt.gz 2020-08-20 21:48 1.5M
refGene.sql 2020-08-20 21:48 1.9K
refFlat.txt.gz 2020-08-20 21:48 1.4M
refFlat.sql 2020-08-20 21:48 1.7K
quality.txt.gz 2008-04-07 15:39 58M
quality.sql 2008-04-07 15:36 1.7K
phastConsElements5way.txt.gz 2008-04-07 15:36 9.8M
phastConsElements5way.sql 2008-04-07 15:36 1.4K
phastCons5way.txt.gz 2008-04-07 15:34 70M
phastCons5way.sql 2008-04-07 15:31 1.7K
nscanPep.txt.gz 2008-04-25 03:16 5.1M
nscanPep.sql 2008-04-25 03:16 1.1K
nscanGene.txt.gz 2008-04-25 03:16 1.4M
nscanGene.sql 2008-04-25 03:16 1.9K
netSusScr2.txt.gz 2010-05-16 11:22 73M
netSusScr2.sql 2010-05-16 11:22 2.0K
netOviAri1.txt.gz 2011-04-25 07:31 80M
netOviAri1.sql 2011-04-25 07:31 2.0K
netOrnAna1.txt.gz 2008-04-07 15:31 18M
netOrnAna1.sql 2008-04-07 15:30 2.2K
netMm9.txt.gz 2008-04-07 15:15 56M
netMm9.sql 2008-04-07 15:12 2.2K
netHg19.txt.gz 2009-09-20 07:41 68M
netHg19.sql 2009-09-20 07:41 2.3K
netCanFam2.txt.gz 2008-04-07 15:25 73M
netCanFam2.sql 2008-04-07 15:22 2.2K
nestedRepeats.txt.gz 2008-04-07 15:22 15M
nestedRepeats.sql 2008-04-07 15:21 1.9K
multiz5waySummary.txt.gz 2008-04-07 15:21 9.8M
multiz5waySummary.sql 2008-04-07 15:21 1.5K
multiz5wayFrames.txt.gz 2008-04-07 15:21 7.7M
multiz5wayFrames.sql 2008-04-07 15:21 1.7K
multiz5way.txt.gz 2008-04-07 15:19 91M
multiz5way.sql 2008-04-07 15:16 1.4K
mrnaOrientInfo.txt.gz 2020-08-20 21:48 591K
mrnaOrientInfo.sql 2020-08-20 21:48 1.8K
microsat.txt.gz 2015-08-23 10:14 299K
microsat.sql 2015-08-23 10:14 1.5K
mgcGenes.txt.gz 2020-03-01 04:52 803K
mgcGenes.sql 2020-03-01 04:52 1.9K
mgcFullMrna.txt.gz 2020-03-01 04:52 908K
mgcFullMrna.sql 2020-03-01 04:52 2.1K
intronEst.txt.gz 2016-06-05 09:03 37M
intronEst.sql 2016-06-05 09:03 2.1K
history.txt.gz 2008-04-07 15:10 742
history.sql 2008-04-07 15:10 1.4K
hgFindSpec.txt.gz 2023-03-28 13:46 1.0K
hgFindSpec.sql 2023-03-28 13:46 1.8K
grp.txt.gz 2014-03-02 03:37 208
grp.sql 2014-03-02 03:37 1.4K
gold.txt.gz 2008-04-07 15:10 2.3M
gold.sql 2008-04-07 15:10 1.6K
genscanPep.txt.gz 2010-10-31 13:25 11M
genscanPep.sql 2010-10-31 13:25 1.3K
genscan.txt.gz 2008-04-07 15:10 3.2M
genscan.sql 2008-04-07 15:10 1.6K
gc5Base.txt.gz 2008-04-07 15:10 11M
gc5Base.sql 2008-04-07 15:09 1.7K
gbLoaded.txt.gz 2020-08-20 21:54 43K
gbLoaded.sql 2020-08-20 21:54 1.6K
gap.txt.gz 2008-04-07 15:04 1.0M
gap.sql 2008-04-07 15:04 1.5K
extFile.txt.gz 2008-04-07 14:51 85
extFile.sql 2008-04-07 14:51 1.3K
estOrientInfo.txt.gz 2016-06-05 09:04 20M
estOrientInfo.sql 2016-06-05 09:04 1.8K
ensemblToGeneName.txt.gz 2011-10-03 07:42 199K
ensemblToGeneName.sql 2011-10-03 07:42 1.3K
ensemblSource.txt.gz 2011-10-03 07:42 119K
ensemblSource.sql 2011-10-03 07:42 1.3K
ensPep.txt.gz 2011-03-14 08:25 7.3M
ensPep.sql 2011-03-14 08:25 1.3K
ensGtp.txt.gz 2011-03-14 08:23 323K
ensGtp.sql 2011-03-14 08:23 1.4K
ensGene.txt.gz 2011-03-14 08:23 2.4M
ensGene.sql 2011-03-14 08:23 1.9K
cytoBandIdeo.txt.gz 2013-08-11 03:45 56K
cytoBandIdeo.sql 2013-08-11 03:45 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 08:32 889K
cpgIslandExtUnmasked.sql 2014-06-01 08:32 1.7K
cpgIslandExt.txt.gz 2008-04-07 15:04 805K
cpgIslandExt.sql 2008-04-07 15:04 1.6K
chromInfo.txt.gz 2008-04-07 15:04 60K
chromInfo.sql 2008-04-07 15:04 1.2K
chainSusScr2Link.txt.gz 2010-05-16 11:47 12G
chainSusScr2Link.sql 2010-05-16 11:22 1.5K
chainSusScr2.txt.gz 2010-05-16 11:07 3.0G
chainSusScr2.sql 2010-05-16 11:01 1.6K
chainOviAri1Link.txt.gz 2011-04-25 07:49 4.3G
chainOviAri1Link.sql 2011-04-25 07:32 1.5K
chainOviAri1.txt.gz 2011-04-25 08:52 2.3G
chainOviAri1.sql 2011-04-25 08:41 1.6K
chainOrnAna1Link.txt.gz 2008-04-07 14:58 249M
chainOrnAna1Link.sql 2008-04-07 14:51 1.4K
chainOrnAna1.txt.gz 2008-04-07 14:50 45M
chainOrnAna1.sql 2008-04-07 14:49 1.7K
chainMm9Link.txt.gz 2008-04-07 14:35 497M
chainMm9Link.sql 2008-04-07 14:20 1.4K
chainMm9.txt.gz 2008-04-07 14:19 64M
chainMm9.sql 2008-04-07 14:17 1.6K
chainHg19Link.txt.gz 2009-09-20 07:36 968M
chainHg19Link.sql 2009-09-20 07:34 1.5K
chainHg19.txt.gz 2009-09-20 07:33 234M
chainHg19.sql 2009-09-20 07:33 1.8K
chainCanFam2Link.txt.gz 2008-04-07 12:48 670M
chainCanFam2Link.sql 2008-04-07 12:20 1.4K
chainCanFam2.txt.gz 2008-04-07 12:17 74M
chainCanFam2.sql 2008-04-07 12:14 1.7K
blastHg18KG.txt.gz 2009-12-20 10:21 4.0M
blastHg18KG.sql 2009-12-20 10:21 2.3K
bigFiles.txt.gz 2024-11-24 03:20 33
bigFiles.sql 2024-11-24 03:20 1.4K
augustusGene.txt.gz 2015-07-26 10:13 2.3M
augustusGene.sql 2015-07-26 10:13 1.9K
all_mrna.txt.gz 2020-08-20 21:48 1.6M
all_mrna.sql 2020-08-20 21:48 2.1K
all_est.txt.gz 2016-06-05 09:04 64M
all_est.sql 2016-06-05 09:04 2.1K