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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2014-12-17 12:32 66
bigFiles.txt.gz 2024-04-21 03:17 69
grp.txt.gz 2014-12-17 12:32 205
history.txt.gz 2014-12-17 12:23 537
hgFindSpec_pushedout.txt.gz 2022-11-29 11:10 858
hgFindSpec.txt.gz 2023-03-28 13:46 861
snp148ExceptionDesc.txt.gz 2016-09-25 05:30 1.0K
gc5BaseBw.sql 2014-12-17 12:32 1.3K
snp148Seq.sql 2016-09-25 05:30 1.3K
grp.sql 2014-12-17 12:32 1.3K
chromInfo.sql 2014-12-17 12:32 1.4K
snp148ExceptionDesc.sql 2016-09-25 05:30 1.4K
bigFiles.sql 2024-04-21 03:17 1.4K
chromAlias.sql 2018-02-18 05:20 1.4K
ucscToINSDC.sql 2014-12-17 12:34 1.4K
ucscToRefSeq.sql 2018-02-18 05:20 1.4K
tableDescriptions.sql 2024-04-20 02:03 1.5K
microsat.sql 2015-08-23 10:31 1.5K
windowmaskerSdust.sql 2014-12-17 12:34 1.5K
cytoBandIdeo.sql 2014-12-17 12:32 1.5K
chainRn6Link.sql 2017-03-26 13:33 1.5K
chainHg38Link.sql 2014-12-17 12:24 1.5K
chainMm10Link.sql 2014-12-17 12:29 1.5K
chainEquCab2Link.sql 2015-02-24 10:56 1.5K
genscanSubopt.sql 2014-12-17 12:32 1.6K
history.sql 2014-12-17 12:23 1.6K
tableList.sql 2024-04-21 03:17 1.6K
gap.sql 2014-12-17 12:32 1.6K
gbLoaded.sql 2020-08-20 21:06 1.6K
gold.sql 2014-12-17 12:32 1.7K
genscan.sql 2014-12-17 12:32 1.7K
cpgIslandExt.sql 2014-12-17 12:32 1.7K
chainRn6.sql 2017-03-26 13:25 1.7K
chainHg38.sql 2014-12-17 12:23 1.7K
chainMm10.sql 2014-12-17 12:29 1.7K
chainEquCab2.sql 2015-02-24 10:54 1.7K
cpgIslandExtUnmasked.sql 2014-12-17 12:32 1.7K
refFlat.sql 2020-08-20 21:06 1.7K
snp148CodingDbSnp.sql 2016-09-25 05:29 1.7K
xenoRefFlat.sql 2020-08-20 21:06 1.7K
hgFindSpec.sql 2023-03-28 13:46 1.8K
estOrientInfo.sql 2015-03-02 10:40 1.8K
hgFindSpec_pushedout.sql 2022-11-29 11:10 1.8K
mrnaOrientInfo.sql 2020-08-20 21:06 1.8K
rmsk.sql 2014-12-17 12:33 1.9K
geneid.sql 2015-11-22 13:03 1.9K
sgpGene.sql 2015-08-30 18:40 1.9K
simpleRepeat.sql 2014-12-17 12:34 1.9K
nestedRepeats.sql 2014-12-17 12:32 1.9K
augustusGene.sql 2015-07-26 10:22 1.9K
refGene.sql 2020-08-20 21:06 1.9K
xenoRefGene.sql 2020-08-20 21:06 2.0K
trackDb.sql 2023-03-28 13:46 2.1K
trackDb_pushedout.sql 2022-11-29 11:10 2.1K
netRn6.sql 2017-03-26 13:29 2.1K
netHg38.sql 2014-12-17 12:32 2.1K
netMm10.sql 2014-12-17 12:32 2.1K
netEquCab2.sql 2015-02-24 11:01 2.1K
all_est.sql 2015-03-02 10:39 2.1K
intronEst.sql 2015-03-02 10:39 2.1K
all_mrna.sql 2020-08-20 21:06 2.1K
refSeqAli.sql 2020-08-20 21:06 2.1K
xenoRefSeqAli.sql 2020-08-20 21:06 2.1K
snp148.sql 2016-09-25 05:32 3.0K
snp148Mult.sql 2016-09-25 05:44 3.0K
tableList.txt.gz 2024-04-21 03:17 4.0K
tableDescriptions.txt.gz 2024-04-20 02:03 6.7K
cytoBandIdeo.txt.gz 2014-12-17 12:32 17K
chromInfo.txt.gz 2014-12-17 12:32 17K
ucscToINSDC.txt.gz 2014-12-17 12:34 22K
ucscToRefSeq.txt.gz 2018-02-18 05:20 24K
chromAlias.txt.gz 2018-02-18 05:20 32K
trackDb.txt.gz 2023-03-28 13:46 50K
trackDb_pushedout.txt.gz 2022-11-29 11:10 50K
gbLoaded.txt.gz 2020-08-20 21:06 60K
microsat.txt.gz 2015-08-23 10:31 275K
mrnaOrientInfo.txt.gz 2020-08-20 21:06 583K
cpgIslandExt.txt.gz 2014-12-17 12:32 803K
cpgIslandExtUnmasked.txt.gz 2014-12-17 12:32 922K
gap.txt.gz 2014-12-17 12:32 948K
gold.txt.gz 2014-12-17 12:32 1.3M
refFlat.txt.gz 2020-08-20 21:06 1.4M
refGene.txt.gz 2020-08-20 21:06 1.5M
refSeqAli.txt.gz 2020-08-20 21:06 1.5M
all_mrna.txt.gz 2020-08-20 21:06 1.6M
snp148Mult.txt.gz 2016-09-25 05:44 2.0M
geneid.txt.gz 2015-11-22 13:03 2.2M
augustusGene.txt.gz 2015-07-26 10:22 2.3M
sgpGene.txt.gz 2015-08-30 18:40 2.4M
genscan.txt.gz 2014-12-17 12:32 3.0M
genscanSubopt.txt.gz 2014-12-17 12:32 5.5M
simpleRepeat.txt.gz 2014-12-17 12:34 12M
nestedRepeats.txt.gz 2014-12-17 12:32 16M
estOrientInfo.txt.gz 2015-03-02 10:40 19M
xenoRefFlat.txt.gz 2020-08-20 21:06 29M
xenoRefSeqAli.txt.gz 2020-08-20 21:06 32M
xenoRefGene.txt.gz 2020-08-20 21:06 32M
intronEst.txt.gz 2015-03-02 10:39 37M
netRn6.txt.gz 2017-03-26 13:30 54M
netEquCab2.txt.gz 2015-02-24 11:02 54M
netMm10.txt.gz 2014-12-17 12:33 54M
all_est.txt.gz 2015-03-02 10:39 61M
chainMm10.txt.gz 2014-12-17 12:29 65M
netHg38.txt.gz 2014-12-17 12:32 66M
snp148CodingDbSnp.txt.gz 2016-09-25 05:29 82M
chainRn6.txt.gz 2017-03-26 13:25 114M
windowmaskerSdust.txt.gz 2014-12-17 12:34 120M
rmsk.txt.gz 2014-12-17 12:33 141M
chainHg38.txt.gz 2014-12-17 12:23 237M
chainEquCab2.txt.gz 2015-02-24 10:54 241M
chainMm10Link.txt.gz 2014-12-17 12:30 494M
snp148Seq.txt.gz 2016-09-25 05:30 601M
chainRn6Link.txt.gz 2017-03-26 13:45 653M
chainHg38Link.txt.gz 2014-12-17 12:25 1.0G
chainEquCab2Link.txt.gz 2015-02-24 10:57 1.2G
snp148.txt.gz 2016-09-25 05:37 1.6G