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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
xenoRefSeqAli.txt.gz 2019-07-25 17:02 30M
xenoRefSeqAli.sql 2019-07-25 17:02 2.1K
xenoRefGene.txt.gz 2019-07-25 17:02 31M
xenoRefGene.sql 2019-07-25 17:02 1.9K
xenoRefFlat.txt.gz 2019-07-25 17:02 28M
xenoRefFlat.sql 2019-07-25 17:01 1.7K
windowmaskerSdust.txt.gz 2019-07-25 17:01 138M
windowmaskerSdust.sql 2019-07-25 17:01 1.5K
ucscToRefSeq.txt.gz 2019-07-25 17:01 40K
ucscToRefSeq.sql 2019-07-25 17:01 1.4K
ucscToINSDC.txt.gz 2019-07-25 17:01 41K
ucscToINSDC.sql 2019-07-25 17:01 1.4K
trackDb.txt.gz 2024-07-25 09:34 69K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-12-08 03:05 3.4K
tableList.sql 2024-12-08 03:05 1.6K
tableDescriptions.txt.gz 2024-12-07 02:04 6.3K
tableDescriptions.sql 2024-12-07 02:04 1.5K
simpleRepeat.txt.gz 2019-07-25 16:51 11M
simpleRepeat.sql 2019-07-25 16:51 1.9K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
rmsk.txt.gz 2019-07-25 16:51 107M
rmsk.sql 2019-07-25 16:50 1.9K
refSeqAli.txt.gz 2019-07-25 16:50 132K
refSeqAli.sql 2019-07-25 16:50 2.1K
refGene.txt.gz 2019-07-25 17:01 133K
refGene.sql 2019-07-25 17:01 1.9K
refFlat.txt.gz 2019-07-25 17:01 122K
refFlat.sql 2019-07-25 17:01 1.7K
netMm39.txt.gz 2020-11-24 19:09 68M
netMm39.sql 2020-11-24 19:09 2.1K
netMm10.txt.gz 2019-07-25 17:01 68M
netMm10.sql 2019-07-25 17:00 2.1K
netHg38.txt.gz 2019-07-25 17:00 53M
netHg38.sql 2019-07-25 17:00 2.1K
nestedRepeats.txt.gz 2019-07-25 16:56 12M
nestedRepeats.sql 2019-07-25 16:56 1.9K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.3M
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.7M
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 12M
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.9M
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 127K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 418K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:27 3.8M
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
mrnaOrientInfo.txt.gz 2019-07-25 16:51 470K
mrnaOrientInfo.sql 2019-07-25 16:51 1.8K
microsat.txt.gz 2019-07-25 17:01 119K
microsat.sql 2019-07-25 17:01 1.5K
intronEst.txt.gz 2019-07-25 17:02 962K
intronEst.sql 2019-07-25 17:02 2.1K
history.txt.gz 2019-07-25 17:02 736
history.sql 2019-07-25 17:02 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2019-07-25 17:01 213
grp.sql 2019-07-25 17:01 1.3K
gold.txt.gz 2019-07-25 17:02 182K
gold.sql 2019-07-25 17:02 1.7K
genscan.txt.gz 2019-07-25 17:02 3.2M
genscan.sql 2019-07-25 17:02 1.7K
gc5BaseBw.txt.gz 2019-07-25 17:01 66
gc5BaseBw.sql 2019-07-25 17:01 1.3K
gbLoaded.txt.gz 2019-07-25 17:01 10K
gbLoaded.sql 2019-07-25 17:01 1.6K
gap.txt.gz 2019-07-25 17:01 86K
gap.sql 2019-07-25 17:01 1.6K
extNcbiRefSeq.txt.gz 2020-05-10 03:27 91
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
estOrientInfo.txt.gz 2019-07-25 17:01 517K
estOrientInfo.sql 2019-07-25 17:01 1.8K
ensemblToGeneName.txt.gz 2021-05-25 14:31 259K
ensemblToGeneName.sql 2021-05-25 14:31 1.4K
ensemblSource.txt.gz 2021-05-25 14:34 188K
ensemblSource.sql 2021-05-25 14:34 1.4K
ensPep.txt.gz 2021-05-25 14:34 16M
ensPep.sql 2021-05-25 14:34 1.3K
ensGtp.txt.gz 2021-05-25 14:31 595K
ensGtp.sql 2021-05-25 14:31 1.4K
ensGene.txt.gz 2021-05-25 14:31 3.3M
ensGene.sql 2021-05-25 14:31 1.9K
cytoBandIdeo.txt.gz 2019-07-25 17:01 26K
cytoBandIdeo.sql 2019-07-25 17:01 1.5K
cpgIslandExtUnmasked.txt.gz 2019-07-25 17:01 967K
cpgIslandExtUnmasked.sql 2019-07-25 17:01 1.7K
cpgIslandExt.txt.gz 2019-07-25 17:01 813K
cpgIslandExt.sql 2019-07-25 17:01 1.7K
chromInfo.txt.gz 2019-07-25 17:01 27K
chromInfo.sql 2019-07-25 17:01 1.4K
chromAlias.txt.gz 2019-07-25 17:00 49K
chromAlias.sql 2019-07-25 17:00 1.4K
chainMm39Link.txt.gz 2020-11-24 19:05 798M
chainMm39Link.sql 2020-11-24 19:05 1.6K
chainMm39.txt.gz 2020-11-24 18:59 127M
chainMm39.sql 2020-11-24 18:59 1.7K
chainMm10Link.txt.gz 2019-07-25 16:57 631M
chainMm10Link.sql 2019-07-25 16:57 1.5K
chainMm10.txt.gz 2019-07-25 16:56 78M
chainMm10.sql 2019-07-25 16:56 1.7K
chainHg38Link.txt.gz 2019-07-25 16:53 884M
chainHg38Link.sql 2019-07-25 16:52 1.5K
chainHg38.txt.gz 2019-07-25 16:51 175M
chainHg38.sql 2019-07-25 16:51 1.7K
bigFiles.txt.gz 2024-12-08 03:05 95
bigFiles.sql 2024-12-08 03:05 1.4K
augustusGene.txt.gz 2019-07-25 16:51 2.4M
augustusGene.sql 2019-07-25 16:51 1.9K
all_mrna.txt.gz 2019-07-25 16:51 1.5M
all_mrna.sql 2019-07-25 16:51 2.1K
all_est.txt.gz 2019-07-25 16:50 1.6M
all_est.sql 2019-07-25 16:50 2.1K