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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
nestedRepeats.sql 2019-06-07 10:37 1.9K
nestedRepeats.txt.gz 2019-06-07 10:37 16M
all_mrna.sql 2019-06-07 10:37 2.1K
all_mrna.txt.gz 2019-06-07 10:37 1.5M
augustusGene.sql 2019-06-07 10:37 1.9K
augustusGene.txt.gz 2019-06-07 10:37 2.3M
mrnaOrientInfo.sql 2019-06-07 10:37 1.8K
mrnaOrientInfo.txt.gz 2019-06-07 10:37 569K
netHg38.sql 2019-06-07 10:37 2.1K
netHg38.txt.gz 2019-06-07 10:38 65M
chainHg38.sql 2019-06-07 10:38 1.7K
chainHg38.txt.gz 2019-06-07 10:38 156M
chainHg38Link.sql 2019-06-07 10:39 1.5K
chainHg38Link.txt.gz 2019-06-07 10:40 796M
netMm10.sql 2019-06-07 10:43 2.1K
netMm10.txt.gz 2019-06-07 10:43 55M
chainMm10.sql 2019-06-07 10:43 1.7K
chainMm10.txt.gz 2019-06-07 10:43 64M
chainMm10Link.sql 2019-06-07 10:43 1.5K
chainMm10Link.txt.gz 2019-06-07 10:44 495M
chromInfo.sql 2019-06-07 10:46 1.4K
chromInfo.txt.gz 2019-06-07 10:46 14K
cpgIslandExt.sql 2019-06-07 10:46 1.7K
cpgIslandExt.txt.gz 2019-06-07 10:46 815K
refFlat.sql 2019-06-07 10:46 1.7K
refFlat.txt.gz 2019-06-07 10:46 1.3M
cpgIslandExtUnmasked.sql 2019-06-07 10:46 1.7K
cpgIslandExtUnmasked.txt.gz 2019-06-07 10:46 936K
grp.sql 2019-06-07 10:46 1.3K
grp.txt.gz 2019-06-07 10:46 213
cytoBandIdeo.sql 2019-06-07 10:46 1.5K
cytoBandIdeo.txt.gz 2019-06-07 10:46 13K
gap.sql 2019-06-07 10:46 1.6K
gap.txt.gz 2019-06-07 10:46 28
gc5BaseBw.sql 2019-06-07 10:46 1.3K
gc5BaseBw.txt.gz 2019-06-07 10:46 66
refGene.sql 2019-06-07 10:46 1.9K
refGene.txt.gz 2019-06-07 10:46 1.4M
refSeqAli.sql 2019-06-07 10:46 2.1K
refSeqAli.txt.gz 2019-06-07 10:46 1.4M
rmsk.sql 2019-06-07 10:46 1.9K
rmsk.txt.gz 2019-06-07 10:46 142M
genscan.sql 2019-06-07 10:47 1.7K
genscan.txt.gz 2019-06-07 10:47 3.0M
gold.sql 2019-06-07 10:47 1.7K
gold.txt.gz 2019-06-07 10:47 27K
simpleRepeat.sql 2019-06-07 10:47 1.9K
simpleRepeat.txt.gz 2019-06-07 10:47 15M
history.sql 2019-06-07 10:47 1.6K
history.txt.gz 2019-06-07 10:47 912
microsat.sql 2019-06-07 10:47 1.5K
microsat.txt.gz 2019-06-07 10:47 278K
ucscToINSDC.sql 2019-06-07 10:47 1.4K
ucscToINSDC.txt.gz 2019-06-07 10:47 20K
ucscToRefSeq.sql 2019-06-07 10:47 1.4K
ucscToRefSeq.txt.gz 2019-06-07 10:47 19K
windowmaskerSdust.sql 2019-06-07 10:47 1.5K
windowmaskerSdust.txt.gz 2019-06-07 10:47 119M
xenoRefFlat.sql 2019-06-07 10:47 1.7K
xenoRefFlat.txt.gz 2019-06-07 10:47 20M
xenoRefGene.sql 2019-06-07 10:47 1.9K
xenoRefGene.txt.gz 2019-06-07 10:47 21M
xenoRefSeqAli.sql 2019-06-07 10:47 2.1K
xenoRefSeqAli.txt.gz 2019-06-07 10:47 21M
all_est.sql 2019-06-16 03:21 2.1K
all_est.txt.gz 2019-06-16 03:21 58M
estOrientInfo.sql 2019-06-16 03:21 1.8K
estOrientInfo.txt.gz 2019-06-16 03:21 18M
gbLoaded.sql 2019-06-16 03:21 1.6K
gbLoaded.txt.gz 2019-06-16 03:21 4.2K
intronEst.sql 2019-06-16 03:21 2.1K
intronEst.txt.gz 2019-06-16 03:21 37M
chromAlias.sql 2020-04-12 03:25 1.4K
chromAlias.txt.gz 2020-04-12 03:25 21K
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:26 3.8M
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 441K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4M
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.3M
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 13M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.1M
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 89
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.1M
chainMm39.sql 2020-11-23 19:20 1.7K
chainMm39.txt.gz 2020-11-23 19:20 68M
chainMm39Link.sql 2020-11-23 19:23 1.6K
chainMm39Link.txt.gz 2020-11-23 19:23 502M
netMm39.sql 2020-11-23 19:26 2.1K
netMm39.txt.gz 2020-11-23 19:26 55M
ensGene.sql 2021-05-25 14:20 1.9K
ensGene.txt.gz 2021-05-25 14:20 2.9M
ensGtp.sql 2021-05-25 14:20 1.4K
ensGtp.txt.gz 2021-05-25 14:20 507K
ensemblToGeneName.sql 2021-05-25 14:20 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:20 245K
ensemblSource.sql 2021-05-25 14:22 1.4K
ensemblSource.txt.gz 2021-05-25 14:22 134K
ensPep.sql 2021-05-25 14:22 1.3K
ensPep.txt.gz 2021-05-25 14:22 13M
crisprAllTargets.sql 2022-03-20 13:48 1.3K
crisprAllTargets.txt.gz 2022-03-20 13:48 69
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 60K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
tableDescriptions.sql 2024-11-09 02:04 1.4K
tableDescriptions.txt.gz 2024-11-09 02:04 6.3K
tableList.sql 2024-11-10 03:05 1.6K
tableList.txt.gz 2024-11-10 03:05 3.5K
bigFiles.sql 2024-11-10 03:05 1.4K
bigFiles.txt.gz 2024-11-10 03:05 119