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 -
chainHg38Link.txt.gz 2019-06-07 10:40 796M
chainMm39Link.txt.gz 2020-11-23 19:23 502M
chainMm10Link.txt.gz 2019-06-07 10:44 495M
chainHg38.txt.gz 2019-06-07 10:38 156M
rmsk.txt.gz 2019-06-07 10:46 142M
windowmaskerSdust.txt.gz 2019-06-07 10:47 119M
chainMm39.txt.gz 2020-11-23 19:20 68M
netHg38.txt.gz 2019-06-07 10:38 65M
chainMm10.txt.gz 2019-06-07 10:43 64M
all_est.txt.gz 2019-06-16 03:21 58M
netMm39.txt.gz 2020-11-23 19:26 55M
netMm10.txt.gz 2019-06-07 10:43 55M
intronEst.txt.gz 2019-06-16 03:21 37M
xenoRefGene.txt.gz 2019-06-07 10:47 21M
xenoRefSeqAli.txt.gz 2019-06-07 10:47 21M
xenoRefFlat.txt.gz 2019-06-07 10:47 20M
estOrientInfo.txt.gz 2019-06-16 03:21 18M
nestedRepeats.txt.gz 2019-06-07 10:37 16M
simpleRepeat.txt.gz 2019-06-07 10:47 15M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 13M
ensPep.txt.gz 2021-05-25 14:22 13M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M
ncbiRefSeq.txt.gz 2020-05-10 03:26 3.8M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.1M
genscan.txt.gz 2019-06-07 10:47 3.0M
ensGene.txt.gz 2021-05-25 14:20 2.9M
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.3M
augustusGene.txt.gz 2019-06-07 10:37 2.3M
all_mrna.txt.gz 2019-06-07 10:37 1.5M
refGene.txt.gz 2019-06-07 10:46 1.4M
refSeqAli.txt.gz 2019-06-07 10:46 1.4M
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4M
refFlat.txt.gz 2019-06-07 10:46 1.3M
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.1M
cpgIslandExtUnmasked.txt.gz 2019-06-07 10:46 936K
cpgIslandExt.txt.gz 2019-06-07 10:46 815K
mrnaOrientInfo.txt.gz 2019-06-07 10:37 569K
ensGtp.txt.gz 2021-05-25 14:20 507K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 441K
microsat.txt.gz 2019-06-07 10:47 278K
ensemblToGeneName.txt.gz 2021-05-25 14:20 245K
ensemblSource.txt.gz 2021-05-25 14:22 134K
trackDb.txt.gz 2024-01-31 15:13 60K
gold.txt.gz 2019-06-07 10:47 27K
chromAlias.txt.gz 2020-04-12 03:25 21K
ucscToINSDC.txt.gz 2019-06-07 10:47 20K
ucscToRefSeq.txt.gz 2019-06-07 10:47 19K
chromInfo.txt.gz 2019-06-07 10:46 14K
cytoBandIdeo.txt.gz 2019-06-07 10:46 13K
tableDescriptions.txt.gz 2024-12-07 02:04 6.3K
gbLoaded.txt.gz 2019-06-16 03:21 4.2K
tableList.txt.gz 2024-12-08 03:05 3.5K
xenoRefSeqAli.sql 2019-06-07 10:47 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
netMm39.sql 2020-11-23 19:26 2.1K
refSeqAli.sql 2019-06-07 10:46 2.1K
all_mrna.sql 2019-06-07 10:37 2.1K
intronEst.sql 2019-06-16 03:21 2.1K
all_est.sql 2019-06-16 03:21 2.1K
netMm10.sql 2019-06-07 10:43 2.1K
netHg38.sql 2019-06-07 10:37 2.1K
trackDb.sql 2024-01-31 15:13 2.1K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ensGene.sql 2021-05-25 14:20 1.9K
augustusGene.sql 2019-06-07 10:37 1.9K
xenoRefGene.sql 2019-06-07 10:47 1.9K
nestedRepeats.sql 2019-06-07 10:37 1.9K
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
simpleRepeat.sql 2019-06-07 10:47 1.9K
refGene.sql 2019-06-07 10:46 1.9K
rmsk.sql 2019-06-07 10:46 1.9K
mrnaOrientInfo.sql 2019-06-07 10:37 1.8K
estOrientInfo.sql 2019-06-16 03:21 1.8K
hgFindSpec.sql 2024-01-31 15:13 1.8K
chainMm39.sql 2020-11-23 19:20 1.7K
xenoRefFlat.sql 2019-06-07 10:47 1.7K
cpgIslandExtUnmasked.sql 2019-06-07 10:46 1.7K
refFlat.sql 2019-06-07 10:46 1.7K
chainMm10.sql 2019-06-07 10:43 1.7K
chainHg38.sql 2019-06-07 10:38 1.7K
cpgIslandExt.sql 2019-06-07 10:46 1.7K
genscan.sql 2019-06-07 10:47 1.7K
gold.sql 2019-06-07 10:47 1.7K
gap.sql 2019-06-07 10:46 1.6K
tableList.sql 2024-12-08 03:05 1.6K
gbLoaded.sql 2019-06-16 03:21 1.6K
history.sql 2019-06-07 10:47 1.6K
chainMm39Link.sql 2020-11-23 19:23 1.6K
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
chainMm10Link.sql 2019-06-07 10:43 1.5K
chainHg38Link.sql 2019-06-07 10:39 1.5K
cytoBandIdeo.sql 2019-06-07 10:46 1.5K
windowmaskerSdust.sql 2019-06-07 10:47 1.5K
microsat.sql 2019-06-07 10:47 1.5K
tableDescriptions.sql 2024-12-07 02:04 1.5K
ensGtp.sql 2021-05-25 14:20 1.4K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
ucscToRefSeq.sql 2019-06-07 10:47 1.4K
ucscToINSDC.sql 2019-06-07 10:47 1.4K
chromAlias.sql 2020-04-12 03:25 1.4K
ensemblToGeneName.sql 2021-05-25 14:20 1.4K
bigFiles.sql 2024-12-08 03:05 1.4K
chromInfo.sql 2019-06-07 10:46 1.4K
ensemblSource.sql 2021-05-25 14:22 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
grp.sql 2019-06-07 10:46 1.3K
ensPep.sql 2021-05-25 14:22 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
crisprAllTargets.sql 2022-03-20 13:48 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
gc5BaseBw.sql 2019-06-07 10:46 1.3K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
history.txt.gz 2019-06-07 10:47 912
grp.txt.gz 2019-06-07 10:46 213
bigFiles.txt.gz 2024-12-08 03:05 119
extNcbiRefSeq.txt.gz 2020-05-10 03:26 89
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
crisprAllTargets.txt.gz 2022-03-20 13:48 69
gc5BaseBw.txt.gz 2019-06-07 10:46 66
gap.txt.gz 2019-06-07 10:46 28