This directory contains a dump of the UCSC genome annotation database for
the Oct. 2010 (BGI CR_1.0/rheMac3) assembly of the rhesus genome (rheMac3,
Beijing Genomics Institute, Shenzhen (GCA_000230795.1)). The annotations
were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/215
http://www.ncbi.nlm.nih.gov/genome/assembly/310688
http://www.ncbi.nlm.nih.gov/bioproject/51409
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=rheMac3
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.cse.ucsc.edu, then go to
the directory goldenPath/rheMac3/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.cse.ucsc.edu/goldenPath/rheMac3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
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 rheMac3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rheMac3 --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 -
chainRn5.sql 2012-11-21 14:34 1.7K
chainRn5.txt.gz 2012-11-21 14:34 49M
netPonAbe2.sql 2012-11-21 14:34 2.1K
netPonAbe2.txt.gz 2012-11-21 14:34 36M
all_est.sql 2012-11-21 14:34 2.1K
all_est.txt.gz 2012-11-21 14:34 3.5M
chainPonAbe2.sql 2012-11-21 14:35 1.7K
chainPonAbe2.txt.gz 2012-11-21 14:35 266M
chainPonAbe2Link.sql 2012-11-21 14:36 1.6K
chainPonAbe2Link.txt.gz 2012-11-21 14:37 817M
chainPanTro4Link.sql 2012-11-21 14:42 1.6K
chainPanTro4Link.txt.gz 2012-11-21 14:42 165M
chainRn5Link.sql 2012-11-21 14:43 1.5K
chainRn5Link.txt.gz 2012-11-21 14:43 447M
chainMm10.sql 2012-11-21 14:45 1.7K
chainMm10.txt.gz 2012-11-21 14:45 60M
chainMm10Link.sql 2012-11-21 14:47 1.5K
chainMm10Link.txt.gz 2012-11-21 14:48 474M
gc5BaseBw.sql 2012-11-21 14:50 1.3K
gc5BaseBw.txt.gz 2012-11-21 14:50 63
netPanTro4.sql 2012-11-21 14:50 2.1K
netPanTro4.txt.gz 2012-11-21 14:50 28M
chainGorGor3Link.sql 2012-11-21 14:50 1.6K
chainGorGor3Link.txt.gz 2012-11-21 14:51 646M
chainPanTro4.sql 2012-11-21 14:53 1.7K
chainPanTro4.txt.gz 2012-11-21 14:53 15M
netGorGor3.sql 2012-11-21 14:53 2.1K
netGorGor3.txt.gz 2012-11-21 14:53 36M
chainCalJac3Link.sql 2012-11-21 14:53 1.6K
chainCalJac3Link.txt.gz 2012-11-21 14:53 221M
chainGorGor3.sql 2012-11-21 14:54 1.7K
chainGorGor3.txt.gz 2012-11-21 14:55 218M
gold.sql 2012-11-21 14:55 1.7K
gold.txt.gz 2012-11-21 14:55 539K
chainMonDom5.sql 2012-11-21 14:55 1.7K
chainMonDom5.txt.gz 2012-11-21 14:56 539M
gap.sql 2012-11-21 14:58 1.6K
gap.txt.gz 2012-11-21 14:58 5.2M
netMonDom5.sql 2012-11-21 14:58 2.1K
netMonDom5.txt.gz 2012-11-21 14:58 18M
chainHg19Link.sql 2012-11-21 14:58 1.5K
chainHg19Link.txt.gz 2012-11-21 14:58 168M
chainMonDom5Link.sql 2012-11-21 14:59 1.6K
ctgPos2.sql 2012-11-21 14:59 1.5K
ctgPos2.txt.gz 2012-11-21 14:59 64K
chainMonDom5Link.txt.gz 2012-11-21 15:01 1.3G
chainHg19.sql 2012-11-21 15:07 1.7K
chainHg19.txt.gz 2012-11-21 15:07 15M
rmsk.sql 2012-11-21 15:07 1.9K
rmsk.txt.gz 2012-11-21 15:07 134M
cpgIslandExt.sql 2012-11-21 15:08 1.7K
cpgIslandExt.txt.gz 2012-11-21 15:08 546K
genscan.sql 2012-11-21 15:08 1.7K
genscan.txt.gz 2012-11-21 15:08 2.8M
history.sql 2012-11-21 15:08 1.6K
history.txt.gz 2012-11-21 15:08 837
estOrientInfo.sql 2012-11-21 15:09 1.8K
estOrientInfo.txt.gz 2012-11-21 15:09 776K
netCalJac3.sql 2012-11-21 15:09 2.1K
netCalJac3.txt.gz 2012-11-21 15:09 46M
chainCalJac3.sql 2012-11-21 15:09 1.7K
chainCalJac3.txt.gz 2012-11-21 15:09 13M
chromInfo.sql 2012-11-21 15:09 1.4K
chromInfo.txt.gz 2012-11-21 15:09 118K
simpleRepeat.sql 2012-11-21 15:09 1.9K
simpleRepeat.txt.gz 2012-11-21 15:09 24M
netHg19.sql 2012-11-21 15:10 2.1K
netHg19.txt.gz 2012-11-21 15:10 26M
nestedRepeats.sql 2012-11-21 15:10 1.9K
nestedRepeats.txt.gz 2012-11-21 15:10 17M
intronEst.sql 2012-11-21 15:10 2.1K
intronEst.txt.gz 2012-11-21 15:10 2.1M
netRn5.sql 2012-11-21 15:11 2.1K
netRn5.txt.gz 2012-11-21 15:11 70M
netMm10.sql 2012-11-21 15:12 2.1K
netMm10.txt.gz 2012-11-21 15:12 70M
windowmaskerSdust.sql 2012-11-21 15:12 1.5K
windowmaskerSdust.txt.gz 2012-11-21 15:12 145M
cytoBandIdeo.sql 2013-04-28 21:17 1.5K
cytoBandIdeo.txt.gz 2013-04-28 21:17 113K
ucscToINSDC.sql 2013-09-15 18:55 1.4K
ucscToINSDC.txt.gz 2013-09-15 18:55 188K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 19:17 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:17 1.1M
netHg38.sql 2015-05-18 07:55 2.1K
netHg38.txt.gz 2015-05-18 07:55 26M
chainHg38Link.sql 2015-05-18 07:55 1.5K
chainHg38Link.txt.gz 2015-05-18 07:55 176M
chainHg38.sql 2015-05-18 07:56 1.7K
chainHg38.txt.gz 2015-05-18 07:56 16M
chainTarSyr2.sql 2015-05-25 09:10 1.7K
chainTarSyr2.txt.gz 2015-05-25 09:10 266M
chainTarSyr2Link.sql 2015-05-25 09:11 1.5K
chainTarSyr2Link.txt.gz 2015-05-25 09:12 1.1G
netTarSyr2.sql 2015-05-25 09:16 2.1K
netTarSyr2.txt.gz 2015-05-25 09:16 69M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.1M
microsat.sql 2015-08-24 00:53 1.5K
microsat.txt.gz 2015-08-24 00:53 262K
geneid.sql 2015-11-22 21:02 1.9K
geneid.txt.gz 2015-11-22 21:02 2.6M
all_mrna.sql 2020-09-01 09:22 2.1K
all_mrna.txt.gz 2020-09-01 09:22 16M
xenoMrna.sql 2020-09-01 09:22 2.1K
xenoMrna.txt.gz 2020-09-01 09:22 323M
refGene.sql 2020-09-01 09:22 1.9K
refGene.txt.gz 2020-09-01 09:22 571K
refFlat.sql 2020-09-01 09:22 1.7K
refFlat.txt.gz 2020-09-01 09:22 526K
xenoRefGene.sql 2020-09-01 09:22 2.0K
xenoRefGene.txt.gz 2020-09-01 09:22 33M
xenoRefFlat.sql 2020-09-01 09:22 1.7K
xenoRefFlat.txt.gz 2020-09-01 09:22 29M
mrnaOrientInfo.sql 2020-09-01 09:22 1.8K
mrnaOrientInfo.txt.gz 2020-09-01 09:22 4.2M
refSeqAli.sql 2020-09-01 09:22 2.1K
refSeqAli.txt.gz 2020-09-01 09:22 588K
xenoRefSeqAli.sql 2020-09-01 09:22 2.1K
xenoRefSeqAli.txt.gz 2020-09-01 09:22 34M
gbLoaded.sql 2020-09-01 09:22 1.6K
gbLoaded.txt.gz 2020-09-01 09:22 81K
trackDb.sql 2023-03-28 13:52 2.1K
trackDb.txt.gz 2023-03-28 13:52 34K
hgFindSpec.sql 2023-03-28 13:52 1.8K
hgFindSpec.txt.gz 2023-03-28 13:52 778
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 5.5K
tableList.sql 2024-12-08 03:34 1.6K
tableList.txt.gz 2024-12-08 03:34 3.9K
bigFiles.sql 2024-12-08 03:34 1.4K
bigFiles.txt.gz 2024-12-08 03:34 68