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