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 -
all_est.sql 02-Mar-2015 10:39 2.1K
all_est.txt.gz 02-Mar-2015 10:39 61M
all_mrna.sql 09-Jul-2017 07:43 2.1K
all_mrna.txt.gz 09-Jul-2017 07:43 1.5M
augustusGene.sql 26-Jul-2015 10:22 1.9K
augustusGene.txt.gz 26-Jul-2015 10:22 2.3M
bigFiles.sql 09-Jul-2017 07:43 1.4K
bigFiles.txt.gz 09-Jul-2017 07:43 69
chainEquCab2.sql 24-Feb-2015 10:54 1.7K
chainEquCab2.txt.gz 24-Feb-2015 10:54 241M
chainEquCab2Link.sql 24-Feb-2015 10:56 1.5K
chainEquCab2Link.txt.gz 24-Feb-2015 10:57 1.2G
chainHg38.sql 17-Dec-2014 12:23 1.7K
chainHg38.txt.gz 17-Dec-2014 12:23 237M
chainHg38Link.sql 17-Dec-2014 12:24 1.5K
chainHg38Link.txt.gz 17-Dec-2014 12:25 1.0G
chainMm10.sql 17-Dec-2014 12:29 1.7K
chainMm10.txt.gz 17-Dec-2014 12:29 65M
chainMm10Link.sql 17-Dec-2014 12:29 1.5K
chainMm10Link.txt.gz 17-Dec-2014 12:30 494M
chainRn6.sql 26-Mar-2017 13:25 1.7K
chainRn6.txt.gz 26-Mar-2017 13:25 114M
chainRn6Link.sql 26-Mar-2017 13:33 1.5K
chainRn6Link.txt.gz 26-Mar-2017 13:45 653M
chromInfo.sql 17-Dec-2014 12:32 1.4K
chromInfo.txt.gz 17-Dec-2014 12:32 17K
cpgIslandExt.sql 17-Dec-2014 12:32 1.7K
cpgIslandExt.txt.gz 17-Dec-2014 12:32 803K
cpgIslandExtUnmasked.sql 17-Dec-2014 12:32 1.7K
cpgIslandExtUnmasked.txt.gz 17-Dec-2014 12:32 922K
cytoBandIdeo.sql 17-Dec-2014 12:32 1.5K
cytoBandIdeo.txt.gz 17-Dec-2014 12:32 17K
estOrientInfo.sql 02-Mar-2015 10:40 1.8K
estOrientInfo.txt.gz 02-Mar-2015 10:40 19M
gap.sql 17-Dec-2014 12:32 1.6K
gap.txt.gz 17-Dec-2014 12:32 948K
gbLoaded.sql 09-Jul-2017 07:44 1.6K
gbLoaded.txt.gz 09-Jul-2017 07:44 33K
gc5BaseBw.sql 17-Dec-2014 12:32 1.3K
gc5BaseBw.txt.gz 17-Dec-2014 12:32 66
geneid.sql 22-Nov-2015 13:03 1.9K
geneid.txt.gz 22-Nov-2015 13:03 2.2M
genscan.sql 17-Dec-2014 12:32 1.7K
genscan.txt.gz 17-Dec-2014 12:32 3.0M
genscanSubopt.sql 17-Dec-2014 12:32 1.6K
genscanSubopt.txt.gz 17-Dec-2014 12:32 5.5M
gold.sql 17-Dec-2014 12:32 1.7K
gold.txt.gz 17-Dec-2014 12:32 1.3M
grp.sql 17-Dec-2014 12:32 1.3K
grp.txt.gz 17-Dec-2014 12:32 205
hgFindSpec.sql 09-Jul-2017 07:44 1.7K
hgFindSpec.txt.gz 09-Jul-2017 07:44 728
history.sql 17-Dec-2014 12:23 1.6K
history.txt.gz 17-Dec-2014 12:23 537
intronEst.sql 02-Mar-2015 10:39 2.1K
intronEst.txt.gz 02-Mar-2015 10:39 37M
microsat.sql 23-Aug-2015 10:31 1.5K
microsat.txt.gz 23-Aug-2015 10:31 275K
mrnaOrientInfo.sql 09-Jul-2017 07:44 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 07:44 570K
nestedRepeats.sql 17-Dec-2014 12:32 1.9K
nestedRepeats.txt.gz 17-Dec-2014 12:32 16M
netEquCab2.sql 24-Feb-2015 11:01 2.1K
netEquCab2.txt.gz 24-Feb-2015 11:02 54M
netHg38.sql 17-Dec-2014 12:32 2.1K
netHg38.txt.gz 17-Dec-2014 12:32 66M
netMm10.sql 17-Dec-2014 12:32 2.1K
netMm10.txt.gz 17-Dec-2014 12:33 54M
netRn6.sql 26-Mar-2017 13:29 2.1K
netRn6.txt.gz 26-Mar-2017 13:30 54M
refFlat.sql 09-Jul-2017 07:44 1.7K
refFlat.txt.gz 09-Jul-2017 07:44 1.4M
refGene.sql 09-Jul-2017 07:43 1.9K
refGene.txt.gz 09-Jul-2017 07:43 1.5M
refSeqAli.sql 09-Jul-2017 07:44 2.1K
refSeqAli.txt.gz 09-Jul-2017 07:44 1.5M
rmsk.sql 17-Dec-2014 12:33 1.9K
rmsk.txt.gz 17-Dec-2014 12:33 141M
sgpGene.sql 30-Aug-2015 18:40 1.9K
sgpGene.txt.gz 30-Aug-2015 18:40 2.4M
simpleRepeat.sql 17-Dec-2014 12:34 1.9K
simpleRepeat.txt.gz 17-Dec-2014 12:34 12M
snp148.sql 25-Sep-2016 05:32 3.0K
snp148.txt.gz 25-Sep-2016 05:37 1.6G
snp148CodingDbSnp.sql 25-Sep-2016 05:29 1.7K
snp148CodingDbSnp.txt.gz 25-Sep-2016 05:29 82M
snp148ExceptionDesc.sql 25-Sep-2016 05:30 1.4K
snp148ExceptionDesc.txt.gz 25-Sep-2016 05:30 1.0K
snp148Mult.sql 25-Sep-2016 05:44 3.0K
snp148Mult.txt.gz 25-Sep-2016 05:44 2.0M
snp148Seq.sql 25-Sep-2016 05:30 1.3K
snp148Seq.txt.gz 25-Sep-2016 05:30 601M
tableDescriptions.sql 09-Jul-2017 07:44 1.4K
tableDescriptions.txt.gz 09-Jul-2017 07:44 5.5K
tableList.sql 09-Jul-2017 07:44 1.5K
tableList.txt.gz 09-Jul-2017 07:44 3.8K
trackDb.sql 09-Jul-2017 07:44 2.0K
trackDb.txt.gz 09-Jul-2017 07:44 46K
ucscToINSDC.sql 17-Dec-2014 12:34 1.4K
ucscToINSDC.txt.gz 17-Dec-2014 12:34 22K
windowmaskerSdust.sql 17-Dec-2014 12:34 1.5K
windowmaskerSdust.txt.gz 17-Dec-2014 12:34 120M
xenoRefFlat.sql 09-Jul-2017 07:43 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 07:43 25M
xenoRefGene.sql 09-Jul-2017 07:43 1.9K
xenoRefGene.txt.gz 09-Jul-2017 07:44 28M
xenoRefSeqAli.sql 09-Jul-2017 07:44 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 07:44 25M