This directory contains a dump of the UCSC genome annotation database for the
Jan. 2018 (EquCab3.0/equCab3) assembly of the horse genome
(equCab3, University of Louisville) .
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/145
https://www.ncbi.nlm.nih.gov/genome/assembly/1512011
https://www.ncbi.nlm.nih.gov/bioproject/421018
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=equCab3
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/equCab3/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/equCab3/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/equCab3/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/equCab3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/equCab3/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 equCab3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql equCab3 --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 2019-07-25 16:53 884M
chainMm39Link.txt.gz 2020-11-24 19:05 798M
chainMm10Link.txt.gz 2019-07-25 16:57 631M
chainHg38.txt.gz 2019-07-25 16:51 175M
windowmaskerSdust.txt.gz 2019-07-25 17:01 138M
chainMm39.txt.gz 2020-11-24 18:59 127M
rmsk.txt.gz 2019-07-25 16:51 107M
chainMm10.txt.gz 2019-07-25 16:56 78M
netMm39.txt.gz 2020-11-24 19:09 68M
netMm10.txt.gz 2019-07-25 17:01 68M
netHg38.txt.gz 2019-07-25 17:00 53M
xenoRefGene.txt.gz 2019-07-25 17:02 31M
xenoRefSeqAli.txt.gz 2019-07-25 17:02 30M
xenoRefFlat.txt.gz 2019-07-25 17:02 28M
ensPep.txt.gz 2021-05-25 14:34 16M
nestedRepeats.txt.gz 2019-07-25 16:56 12M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 12M
simpleRepeat.txt.gz 2019-07-25 16:51 11M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.3M
ncbiRefSeq.txt.gz 2020-05-10 03:27 3.8M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.7M
ensGene.txt.gz 2021-05-25 14:31 3.3M
genscan.txt.gz 2019-07-25 17:02 3.2M
augustusGene.txt.gz 2019-07-25 16:51 2.4M
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.9M
all_est.txt.gz 2019-07-25 16:50 1.6M
all_mrna.txt.gz 2019-07-25 16:51 1.5M
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M
cpgIslandExtUnmasked.txt.gz 2019-07-25 17:01 967K
intronEst.txt.gz 2019-07-25 17:02 962K
cpgIslandExt.txt.gz 2019-07-25 17:01 813K
ensGtp.txt.gz 2021-05-25 14:31 595K
estOrientInfo.txt.gz 2019-07-25 17:01 517K
mrnaOrientInfo.txt.gz 2019-07-25 16:51 470K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 418K
ensemblToGeneName.txt.gz 2021-05-25 14:31 259K
ensemblSource.txt.gz 2021-05-25 14:34 188K
gold.txt.gz 2019-07-25 17:02 182K
refGene.txt.gz 2019-07-25 17:01 133K
refSeqAli.txt.gz 2019-07-25 16:50 132K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 127K
refFlat.txt.gz 2019-07-25 17:01 122K
microsat.txt.gz 2019-07-25 17:01 119K
gap.txt.gz 2019-07-25 17:01 86K
trackDb.txt.gz 2024-01-31 15:13 54K
chromAlias.txt.gz 2019-07-25 17:00 49K
ucscToINSDC.txt.gz 2019-07-25 17:01 41K
ucscToRefSeq.txt.gz 2019-07-25 17:01 40K
trackDb_pushedout.txt.gz 2023-12-05 13:51 32K
chromInfo.txt.gz 2019-07-25 17:01 27K
cytoBandIdeo.txt.gz 2019-07-25 17:01 26K
gbLoaded.txt.gz 2019-07-25 17:01 10K
tableDescriptions.txt.gz 2024-04-27 02:04 6.3K
tableList.txt.gz 2024-04-28 03:05 3.6K
xenoRefSeqAli.sql 2019-07-25 17:02 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
netMm39.sql 2020-11-24 19:09 2.1K
refSeqAli.sql 2019-07-25 16:50 2.1K
intronEst.sql 2019-07-25 17:02 2.1K
all_mrna.sql 2019-07-25 16:51 2.1K
all_est.sql 2019-07-25 16:50 2.1K
netMm10.sql 2019-07-25 17:00 2.1K
netHg38.sql 2019-07-25 17:00 2.1K
trackDb_pushedout.sql 2023-12-05 13:51 2.1K
trackDb.sql 2024-01-31 15:13 2.1K
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ensGene.sql 2021-05-25 14:31 1.9K
augustusGene.sql 2019-07-25 16:51 1.9K
xenoRefGene.sql 2019-07-25 17:02 1.9K
nestedRepeats.sql 2019-07-25 16:56 1.9K
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
simpleRepeat.sql 2019-07-25 16:51 1.9K
refGene.sql 2019-07-25 17:01 1.9K
rmsk.sql 2019-07-25 16:50 1.9K
hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K
mrnaOrientInfo.sql 2019-07-25 16:51 1.8K
estOrientInfo.sql 2019-07-25 17:01 1.8K
hgFindSpec.sql 2024-01-31 15:13 1.8K
chainMm39.sql 2020-11-24 18:59 1.7K
xenoRefFlat.sql 2019-07-25 17:01 1.7K
cpgIslandExtUnmasked.sql 2019-07-25 17:01 1.7K
refFlat.sql 2019-07-25 17:01 1.7K
chainMm10.sql 2019-07-25 16:56 1.7K
chainHg38.sql 2019-07-25 16:51 1.7K
cpgIslandExt.sql 2019-07-25 17:01 1.7K
genscan.sql 2019-07-25 17:02 1.7K
gold.sql 2019-07-25 17:02 1.7K
gap.sql 2019-07-25 17:01 1.6K
tableList.sql 2024-04-28 03:05 1.6K
gbLoaded.sql 2019-07-25 17:01 1.6K
history.sql 2019-07-25 17:02 1.6K
chainMm39Link.sql 2020-11-24 19:05 1.6K
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
chainMm10Link.sql 2019-07-25 16:57 1.5K
chainHg38Link.sql 2019-07-25 16:52 1.5K
cytoBandIdeo.sql 2019-07-25 17:01 1.5K
windowmaskerSdust.sql 2019-07-25 17:01 1.5K
microsat.sql 2019-07-25 17:01 1.5K
tableDescriptions.sql 2024-04-27 02:04 1.5K
ensGtp.sql 2021-05-25 14:31 1.4K
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
ucscToRefSeq.sql 2019-07-25 17:01 1.4K
ucscToINSDC.sql 2019-07-25 17:01 1.4K
chromAlias.sql 2019-07-25 17:00 1.4K
ensemblToGeneName.sql 2021-05-25 14:31 1.4K
bigFiles.sql 2024-04-28 03:05 1.4K
chromInfo.sql 2019-07-25 17:01 1.4K
ensemblSource.sql 2021-05-25 14:34 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
grp.sql 2019-07-25 17:01 1.3K
ensPep.sql 2021-05-25 14:34 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.3K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
gc5BaseBw.sql 2019-07-25 17:01 1.3K
history.txt.gz 2019-07-25 17:02 736
grp.txt.gz 2019-07-25 17:01 213
bigFiles.txt.gz 2024-04-28 03:05 95
extNcbiRefSeq.txt.gz 2020-05-10 03:27 91
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
gc5BaseBw.txt.gz 2019-07-25 17:01 66