This directory contains a dump of the UCSC genome annotation database for the
Dec. 2009 (UMD_3.1.1/bosTau8) assembly of the cow genome
(bosTau8, University of Maryland Bos_taurus_UMD_3.1.1) .
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/82
http://www.ncbi.nlm.nih.gov/genome/assembly/189361
http://www.ncbi.nlm.nih.gov/bioproject/33843
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=bosTau8
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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/bosTau8/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/bosTau8/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/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 bosTau8 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau8 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
history.sql 2014-12-17 12:23 1.6K
history.txt.gz 2014-12-17 12:23 537
chainHg38.sql 2014-12-17 12:23 1.7K
chainHg38.txt.gz 2014-12-17 12:23 237M
chainHg38Link.sql 2014-12-17 12:24 1.5K
chainHg38Link.txt.gz 2014-12-17 12:25 1.0G
chainMm10.sql 2014-12-17 12:29 1.7K
chainMm10.txt.gz 2014-12-17 12:29 65M
chainMm10Link.sql 2014-12-17 12:29 1.5K
chainMm10Link.txt.gz 2014-12-17 12:30 494M
chromInfo.sql 2014-12-17 12:32 1.4K
chromInfo.txt.gz 2014-12-17 12:32 17K
cpgIslandExt.sql 2014-12-17 12:32 1.7K
cpgIslandExt.txt.gz 2014-12-17 12:32 803K
gc5BaseBw.sql 2014-12-17 12:32 1.3K
gc5BaseBw.txt.gz 2014-12-17 12:32 66
cpgIslandExtUnmasked.sql 2014-12-17 12:32 1.7K
cpgIslandExtUnmasked.txt.gz 2014-12-17 12:32 922K
cytoBandIdeo.sql 2014-12-17 12:32 1.5K
cytoBandIdeo.txt.gz 2014-12-17 12:32 17K
nestedRepeats.sql 2014-12-17 12:32 1.9K
nestedRepeats.txt.gz 2014-12-17 12:32 16M
genscan.sql 2014-12-17 12:32 1.7K
genscan.txt.gz 2014-12-17 12:32 3.0M
genscanSubopt.sql 2014-12-17 12:32 1.6K
genscanSubopt.txt.gz 2014-12-17 12:32 5.5M
gap.sql 2014-12-17 12:32 1.6K
gap.txt.gz 2014-12-17 12:32 948K
gold.sql 2014-12-17 12:32 1.7K
gold.txt.gz 2014-12-17 12:32 1.3M
netHg38.sql 2014-12-17 12:32 2.1K
netHg38.txt.gz 2014-12-17 12:32 66M
grp.sql 2014-12-17 12:32 1.3K
grp.txt.gz 2014-12-17 12:32 205
netMm10.sql 2014-12-17 12:32 2.1K
netMm10.txt.gz 2014-12-17 12:33 54M
rmsk.sql 2014-12-17 12:33 1.9K
rmsk.txt.gz 2014-12-17 12:33 141M
simpleRepeat.sql 2014-12-17 12:34 1.9K
simpleRepeat.txt.gz 2014-12-17 12:34 12M
ucscToINSDC.sql 2014-12-17 12:34 1.4K
ucscToINSDC.txt.gz 2014-12-17 12:34 22K
windowmaskerSdust.sql 2014-12-17 12:34 1.5K
windowmaskerSdust.txt.gz 2014-12-17 12:34 120M
chainEquCab2.sql 2015-02-24 10:54 1.7K
chainEquCab2.txt.gz 2015-02-24 10:54 241M
chainEquCab2Link.sql 2015-02-24 10:56 1.5K
chainEquCab2Link.txt.gz 2015-02-24 10:57 1.2G
netEquCab2.sql 2015-02-24 11:01 2.1K
netEquCab2.txt.gz 2015-02-24 11:02 54M
all_est.sql 2015-03-02 10:39 2.1K
all_est.txt.gz 2015-03-02 10:39 61M
intronEst.sql 2015-03-02 10:39 2.1K
intronEst.txt.gz 2015-03-02 10:39 37M
estOrientInfo.sql 2015-03-02 10:40 1.8K
estOrientInfo.txt.gz 2015-03-02 10:40 19M
augustusGene.sql 2015-07-26 10:22 1.9K
augustusGene.txt.gz 2015-07-26 10:22 2.3M
microsat.sql 2015-08-23 10:31 1.5K
microsat.txt.gz 2015-08-23 10:31 275K
sgpGene.sql 2015-08-30 18:40 1.9K
sgpGene.txt.gz 2015-08-30 18:40 2.4M
geneid.sql 2015-11-22 13:03 1.9K
geneid.txt.gz 2015-11-22 13:03 2.2M
snp148CodingDbSnp.sql 2016-09-25 05:29 1.7K
snp148CodingDbSnp.txt.gz 2016-09-25 05:29 82M
snp148ExceptionDesc.sql 2016-09-25 05:30 1.4K
snp148ExceptionDesc.txt.gz 2016-09-25 05:30 1.0K
snp148Seq.sql 2016-09-25 05:30 1.3K
snp148Seq.txt.gz 2016-09-25 05:30 601M
snp148.sql 2016-09-25 05:32 3.0K
snp148.txt.gz 2016-09-25 05:37 1.6G
snp148Mult.sql 2016-09-25 05:44 3.0K
snp148Mult.txt.gz 2016-09-25 05:44 2.0M
chainRn6.sql 2017-03-26 13:25 1.7K
chainRn6.txt.gz 2017-03-26 13:25 114M
netRn6.sql 2017-03-26 13:29 2.1K
netRn6.txt.gz 2017-03-26 13:30 54M
chainRn6Link.sql 2017-03-26 13:33 1.5K
chainRn6Link.txt.gz 2017-03-26 13:45 653M
chromAlias.sql 2018-02-18 05:20 1.4K
chromAlias.txt.gz 2018-02-18 05:20 32K
ucscToRefSeq.sql 2018-02-18 05:20 1.4K
ucscToRefSeq.txt.gz 2018-02-18 05:20 24K
all_mrna.sql 2020-08-20 21:06 2.1K
all_mrna.txt.gz 2020-08-20 21:06 1.6M
refGene.sql 2020-08-20 21:06 1.9K
refGene.txt.gz 2020-08-20 21:06 1.5M
refFlat.sql 2020-08-20 21:06 1.7K
refFlat.txt.gz 2020-08-20 21:06 1.4M
xenoRefGene.sql 2020-08-20 21:06 2.0K
xenoRefGene.txt.gz 2020-08-20 21:06 32M
xenoRefFlat.sql 2020-08-20 21:06 1.7K
xenoRefFlat.txt.gz 2020-08-20 21:06 29M
mrnaOrientInfo.sql 2020-08-20 21:06 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 21:06 583K
refSeqAli.sql 2020-08-20 21:06 2.1K
refSeqAli.txt.gz 2020-08-20 21:06 1.5M
xenoRefSeqAli.sql 2020-08-20 21:06 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 21:06 32M
gbLoaded.sql 2020-08-20 21:06 1.6K
gbLoaded.txt.gz 2020-08-20 21:06 60K
trackDb_pushedout.sql 2022-11-29 11:10 2.1K
trackDb_pushedout.txt.gz 2022-11-29 11:10 50K
hgFindSpec_pushedout.sql 2022-11-29 11:10 1.8K
hgFindSpec_pushedout.txt.gz 2022-11-29 11:10 858
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 13:46 861
tableDescriptions.sql 2024-04-27 02:03 1.5K
tableDescriptions.txt.gz 2024-04-27 02:03 6.7K
tableList.sql 2024-04-28 03:15 1.6K
tableList.txt.gz 2024-04-28 03:15 4.0K
bigFiles.sql 2024-04-28 03:15 1.4K
bigFiles.txt.gz 2024-04-28 03:15 69