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 -
xenoRefSeqAli.txt.gz 2020-08-20 21:06 32M
xenoRefSeqAli.sql 2020-08-20 21:06 2.1K
xenoRefGene.txt.gz 2020-08-20 21:06 32M
xenoRefGene.sql 2020-08-20 21:06 2.0K
xenoRefFlat.txt.gz 2020-08-20 21:06 29M
xenoRefFlat.sql 2020-08-20 21:06 1.7K
windowmaskerSdust.txt.gz 2014-12-17 12:34 120M
windowmaskerSdust.sql 2014-12-17 12:34 1.5K
ucscToRefSeq.txt.gz 2018-02-18 05:20 24K
ucscToRefSeq.sql 2018-02-18 05:20 1.4K
ucscToINSDC.txt.gz 2014-12-17 12:34 22K
ucscToINSDC.sql 2014-12-17 12:34 1.4K
trackDb.txt.gz 2023-03-28 13:46 50K
trackDb.sql 2023-03-28 13:46 2.1K
tableList.txt.gz 2024-12-08 03:16 3.9K
tableList.sql 2024-12-08 03:16 1.6K
tableDescriptions.txt.gz 2024-12-07 02:03 6.7K
tableDescriptions.sql 2024-12-07 02:03 1.5K
snp148Seq.txt.gz 2016-09-25 05:30 601M
snp148Seq.sql 2016-09-25 05:30 1.3K
snp148Mult.txt.gz 2016-09-25 05:44 2.0M
snp148Mult.sql 2016-09-25 05:44 3.0K
snp148ExceptionDesc.txt.gz 2016-09-25 05:30 1.0K
snp148ExceptionDesc.sql 2016-09-25 05:30 1.4K
snp148CodingDbSnp.txt.gz 2016-09-25 05:29 82M
snp148CodingDbSnp.sql 2016-09-25 05:29 1.7K
snp148.txt.gz 2016-09-25 05:37 1.6G
snp148.sql 2016-09-25 05:32 3.0K
simpleRepeat.txt.gz 2014-12-17 12:34 12M
simpleRepeat.sql 2014-12-17 12:34 1.9K
sgpGene.txt.gz 2015-08-30 18:40 2.4M
sgpGene.sql 2015-08-30 18:40 1.9K
rmsk.txt.gz 2014-12-17 12:33 141M
rmsk.sql 2014-12-17 12:33 1.9K
refSeqAli.txt.gz 2020-08-20 21:06 1.5M
refSeqAli.sql 2020-08-20 21:06 2.1K
refGene.txt.gz 2020-08-20 21:06 1.5M
refGene.sql 2020-08-20 21:06 1.9K
refFlat.txt.gz 2020-08-20 21:06 1.4M
refFlat.sql 2020-08-20 21:06 1.7K
netRn6.txt.gz 2017-03-26 13:30 54M
netRn6.sql 2017-03-26 13:29 2.1K
netMm10.txt.gz 2014-12-17 12:33 54M
netMm10.sql 2014-12-17 12:32 2.1K
netHg38.txt.gz 2014-12-17 12:32 66M
netHg38.sql 2014-12-17 12:32 2.1K
netEquCab2.txt.gz 2015-02-24 11:02 54M
netEquCab2.sql 2015-02-24 11:01 2.1K
nestedRepeats.txt.gz 2014-12-17 12:32 16M
nestedRepeats.sql 2014-12-17 12:32 1.9K
mrnaOrientInfo.txt.gz 2020-08-20 21:06 583K
mrnaOrientInfo.sql 2020-08-20 21:06 1.8K
microsat.txt.gz 2015-08-23 10:31 275K
microsat.sql 2015-08-23 10:31 1.5K
intronEst.txt.gz 2015-03-02 10:39 37M
intronEst.sql 2015-03-02 10:39 2.1K
history.txt.gz 2014-12-17 12:23 537
history.sql 2014-12-17 12:23 1.6K
hgFindSpec.txt.gz 2023-03-28 13:46 861
hgFindSpec.sql 2023-03-28 13:46 1.8K
grp.txt.gz 2014-12-17 12:32 205
grp.sql 2014-12-17 12:32 1.3K
gold.txt.gz 2014-12-17 12:32 1.3M
gold.sql 2014-12-17 12:32 1.7K
genscanSubopt.txt.gz 2014-12-17 12:32 5.5M
genscanSubopt.sql 2014-12-17 12:32 1.6K
genscan.txt.gz 2014-12-17 12:32 3.0M
genscan.sql 2014-12-17 12:32 1.7K
geneid.txt.gz 2015-11-22 13:03 2.2M
geneid.sql 2015-11-22 13:03 1.9K
gc5BaseBw.txt.gz 2014-12-17 12:32 66
gc5BaseBw.sql 2014-12-17 12:32 1.3K
gbLoaded.txt.gz 2020-08-20 21:06 60K
gbLoaded.sql 2020-08-20 21:06 1.6K
gap.txt.gz 2014-12-17 12:32 948K
gap.sql 2014-12-17 12:32 1.6K
estOrientInfo.txt.gz 2015-03-02 10:40 19M
estOrientInfo.sql 2015-03-02 10:40 1.8K
cytoBandIdeo.txt.gz 2014-12-17 12:32 17K
cytoBandIdeo.sql 2014-12-17 12:32 1.5K
cpgIslandExtUnmasked.txt.gz 2014-12-17 12:32 922K
cpgIslandExtUnmasked.sql 2014-12-17 12:32 1.7K
cpgIslandExt.txt.gz 2014-12-17 12:32 803K
cpgIslandExt.sql 2014-12-17 12:32 1.7K
chromInfo.txt.gz 2014-12-17 12:32 17K
chromInfo.sql 2014-12-17 12:32 1.4K
chromAlias.txt.gz 2018-02-18 05:20 32K
chromAlias.sql 2018-02-18 05:20 1.4K
chainRn6Link.txt.gz 2017-03-26 13:45 653M
chainRn6Link.sql 2017-03-26 13:33 1.5K
chainRn6.txt.gz 2017-03-26 13:25 114M
chainRn6.sql 2017-03-26 13:25 1.7K
chainMm10Link.txt.gz 2014-12-17 12:30 494M
chainMm10Link.sql 2014-12-17 12:29 1.5K
chainMm10.txt.gz 2014-12-17 12:29 65M
chainMm10.sql 2014-12-17 12:29 1.7K
chainHg38Link.txt.gz 2014-12-17 12:25 1.0G
chainHg38Link.sql 2014-12-17 12:24 1.5K
chainHg38.txt.gz 2014-12-17 12:23 237M
chainHg38.sql 2014-12-17 12:23 1.7K
chainEquCab2Link.txt.gz 2015-02-24 10:57 1.2G
chainEquCab2Link.sql 2015-02-24 10:56 1.5K
chainEquCab2.txt.gz 2015-02-24 10:54 241M
chainEquCab2.sql 2015-02-24 10:54 1.7K
bigFiles.txt.gz 2024-12-08 03:16 69
bigFiles.sql 2024-12-08 03:16 1.4K
augustusGene.txt.gz 2015-07-26 10:22 2.3M
augustusGene.sql 2015-07-26 10:22 1.9K
all_mrna.txt.gz 2020-08-20 21:06 1.6M
all_mrna.sql 2020-08-20 21:06 2.1K
all_est.txt.gz 2015-03-02 10:39 61M
all_est.sql 2015-03-02 10:39 2.1K