This directory contains a dump of the UCSC genome annotation database for the
Apr. 2018 (ARS-UCD1.2/bosTau9) assembly of the cow genome
(bosTau9, USDA ARS) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/82
https://www.ncbi.nlm.nih.gov/genome/assembly/1677391
https://www.ncbi.nlm.nih.gov/bioproject/391427
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=bosTau9
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.soe.ucsc.edu, then go to
the directory goldenPath/bosTau9/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.soe.ucsc.edu/goldenPath/bosTau9/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 bosTau9 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau9 --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 -
xenoRefSeqAli.txt.gz 2019-06-07 10:47 21M
xenoRefSeqAli.sql 2019-06-07 10:47 2.1K
xenoRefGene.txt.gz 2019-06-07 10:47 21M
xenoRefGene.sql 2019-06-07 10:47 1.9K
xenoRefFlat.txt.gz 2019-06-07 10:47 20M
xenoRefFlat.sql 2019-06-07 10:47 1.7K
windowmaskerSdust.txt.gz 2019-06-07 10:47 119M
windowmaskerSdust.sql 2019-06-07 10:47 1.5K
ucscToRefSeq.txt.gz 2019-06-07 10:47 19K
ucscToRefSeq.sql 2019-06-07 10:47 1.4K
ucscToINSDC.txt.gz 2019-06-07 10:47 20K
ucscToINSDC.sql 2019-06-07 10:47 1.4K
trackDb.txt.gz 2024-01-31 15:13 60K
trackDb.sql 2024-01-31 15:13 2.1K
tableList.txt.gz 2024-11-24 03:04 3.5K
tableList.sql 2024-11-24 03:04 1.6K
tableDescriptions.txt.gz 2024-11-23 02:04 6.3K
tableDescriptions.sql 2024-11-23 02:04 1.5K
simpleRepeat.txt.gz 2019-06-07 10:47 15M
simpleRepeat.sql 2019-06-07 10:47 1.9K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.1M
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
rmsk.txt.gz 2019-06-07 10:46 142M
rmsk.sql 2019-06-07 10:46 1.9K
refSeqAli.txt.gz 2019-06-07 10:46 1.4M
refSeqAli.sql 2019-06-07 10:46 2.1K
refGene.txt.gz 2019-06-07 10:46 1.4M
refGene.sql 2019-06-07 10:46 1.9K
refFlat.txt.gz 2019-06-07 10:46 1.3M
refFlat.sql 2019-06-07 10:46 1.7K
netMm39.txt.gz 2020-11-23 19:26 55M
netMm39.sql 2020-11-23 19:26 2.1K
netMm10.txt.gz 2019-06-07 10:43 55M
netMm10.sql 2019-06-07 10:43 2.1K
netHg38.txt.gz 2019-06-07 10:38 65M
netHg38.sql 2019-06-07 10:37 2.1K
nestedRepeats.txt.gz 2019-06-07 10:37 16M
nestedRepeats.sql 2019-06-07 10:37 1.9K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.1M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 13M
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.3M
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4M
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 441K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:26 3.8M
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
mrnaOrientInfo.txt.gz 2019-06-07 10:37 569K
mrnaOrientInfo.sql 2019-06-07 10:37 1.8K
microsat.txt.gz 2019-06-07 10:47 278K
microsat.sql 2019-06-07 10:47 1.5K
intronEst.txt.gz 2019-06-16 03:21 37M
intronEst.sql 2019-06-16 03:21 2.1K
history.txt.gz 2019-06-07 10:47 912
history.sql 2019-06-07 10:47 1.6K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
hgFindSpec.sql 2024-01-31 15:13 1.8K
grp.txt.gz 2019-06-07 10:46 213
grp.sql 2019-06-07 10:46 1.3K
gold.txt.gz 2019-06-07 10:47 27K
gold.sql 2019-06-07 10:47 1.7K
genscan.txt.gz 2019-06-07 10:47 3.0M
genscan.sql 2019-06-07 10:47 1.7K
gc5BaseBw.txt.gz 2019-06-07 10:46 66
gc5BaseBw.sql 2019-06-07 10:46 1.3K
gbLoaded.txt.gz 2019-06-16 03:21 4.2K
gbLoaded.sql 2019-06-16 03:21 1.6K
gap.txt.gz 2019-06-07 10:46 28
gap.sql 2019-06-07 10:46 1.6K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 89
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
estOrientInfo.txt.gz 2019-06-16 03:21 18M
estOrientInfo.sql 2019-06-16 03:21 1.8K
ensemblToGeneName.txt.gz 2021-05-25 14:20 245K
ensemblToGeneName.sql 2021-05-25 14:20 1.4K
ensemblSource.txt.gz 2021-05-25 14:22 134K
ensemblSource.sql 2021-05-25 14:22 1.4K
ensPep.txt.gz 2021-05-25 14:22 13M
ensPep.sql 2021-05-25 14:22 1.3K
ensGtp.txt.gz 2021-05-25 14:20 507K
ensGtp.sql 2021-05-25 14:20 1.4K
ensGene.txt.gz 2021-05-25 14:20 2.9M
ensGene.sql 2021-05-25 14:20 1.9K
cytoBandIdeo.txt.gz 2019-06-07 10:46 13K
cytoBandIdeo.sql 2019-06-07 10:46 1.5K
crisprAllTargets.txt.gz 2022-03-20 13:48 69
crisprAllTargets.sql 2022-03-20 13:48 1.3K
cpgIslandExtUnmasked.txt.gz 2019-06-07 10:46 936K
cpgIslandExtUnmasked.sql 2019-06-07 10:46 1.7K
cpgIslandExt.txt.gz 2019-06-07 10:46 815K
cpgIslandExt.sql 2019-06-07 10:46 1.7K
chromInfo.txt.gz 2019-06-07 10:46 14K
chromInfo.sql 2019-06-07 10:46 1.4K
chromAlias.txt.gz 2020-04-12 03:25 21K
chromAlias.sql 2020-04-12 03:25 1.4K
chainMm39Link.txt.gz 2020-11-23 19:23 502M
chainMm39Link.sql 2020-11-23 19:23 1.6K
chainMm39.txt.gz 2020-11-23 19:20 68M
chainMm39.sql 2020-11-23 19:20 1.7K
chainMm10Link.txt.gz 2019-06-07 10:44 495M
chainMm10Link.sql 2019-06-07 10:43 1.5K
chainMm10.txt.gz 2019-06-07 10:43 64M
chainMm10.sql 2019-06-07 10:43 1.7K
chainHg38Link.txt.gz 2019-06-07 10:40 796M
chainHg38Link.sql 2019-06-07 10:39 1.5K
chainHg38.txt.gz 2019-06-07 10:38 156M
chainHg38.sql 2019-06-07 10:38 1.7K
bigFiles.txt.gz 2024-11-24 03:04 119
bigFiles.sql 2024-11-24 03:04 1.4K
augustusGene.txt.gz 2019-06-07 10:37 2.3M
augustusGene.sql 2019-06-07 10:37 1.9K
all_mrna.txt.gz 2019-06-07 10:37 1.5M
all_mrna.sql 2019-06-07 10:37 2.1K
all_est.txt.gz 2019-06-16 03:21 58M
all_est.sql 2019-06-16 03:21 2.1K