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.
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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.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;'
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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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2012-11-21 14:50 63
bigFiles.txt.gz 2024-11-17 03:37 68
grp.txt.gz 2014-03-02 04:14 208
hgFindSpec.txt.gz 2023-03-28 13:52 778
history.txt.gz 2012-11-21 15:08 837
gc5BaseBw.sql 2012-11-21 14:50 1.3K
grp.sql 2014-03-02 04:14 1.3K
bigFiles.sql 2024-11-17 03:37 1.4K
chromInfo.sql 2012-11-21 15:09 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToINSDC.sql 2013-09-15 18:55 1.4K
microsat.sql 2015-08-24 00:53 1.5K
windowmaskerSdust.sql 2012-11-21 15:12 1.5K
cytoBandIdeo.sql 2013-04-28 21:17 1.5K
chainRn5Link.sql 2012-11-21 14:43 1.5K
chainHg38Link.sql 2015-05-18 07:55 1.5K
ctgPos2.sql 2012-11-21 14:59 1.5K
chainHg19Link.sql 2012-11-21 14:58 1.5K
chainMm10Link.sql 2012-11-21 14:47 1.5K
chainTarSyr2Link.sql 2015-05-25 09:11 1.5K
chainCalJac3Link.sql 2012-11-21 14:53 1.6K
chainGorGor3Link.sql 2012-11-21 14:50 1.6K
chainMonDom5Link.sql 2012-11-21 14:59 1.6K
chainPanTro4Link.sql 2012-11-21 14:42 1.6K
chainPonAbe2Link.sql 2012-11-21 14:36 1.6K
tableList.sql 2024-11-17 03:37 1.6K
history.sql 2012-11-21 15:08 1.6K
gap.sql 2012-11-21 14:58 1.6K
gbLoaded.sql 2020-09-01 09:22 1.6K
gold.sql 2012-11-21 14:55 1.7K
genscan.sql 2012-11-21 15:08 1.7K
cpgIslandExt.sql 2012-11-21 15:08 1.7K
chainRn5.sql 2012-11-21 14:34 1.7K
chainHg38.sql 2015-05-18 07:56 1.7K
chainHg19.sql 2012-11-21 15:07 1.7K
chainMm10.sql 2012-11-21 14:45 1.7K
chainTarSyr2.sql 2015-05-25 09:10 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 19:17 1.7K
chainCalJac3.sql 2012-11-21 15:09 1.7K
chainGorGor3.sql 2012-11-21 14:54 1.7K
chainMonDom5.sql 2012-11-21 14:55 1.7K
chainPanTro4.sql 2012-11-21 14:53 1.7K
chainPonAbe2.sql 2012-11-21 14:35 1.7K
refFlat.sql 2020-09-01 09:22 1.7K
xenoRefFlat.sql 2020-09-01 09:22 1.7K
hgFindSpec.sql 2023-03-28 13:52 1.8K
estOrientInfo.sql 2012-11-21 15:09 1.8K
mrnaOrientInfo.sql 2020-09-01 09:22 1.8K
rmsk.sql 2012-11-21 15:07 1.9K
geneid.sql 2015-11-22 21:02 1.9K
simpleRepeat.sql 2012-11-21 15:09 1.9K
nestedRepeats.sql 2012-11-21 15:10 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
refGene.sql 2020-09-01 09:22 1.9K
xenoRefGene.sql 2020-09-01 09:22 2.0K
trackDb.sql 2023-03-28 13:52 2.1K
netRn5.sql 2012-11-21 15:11 2.1K
netHg38.sql 2015-05-18 07:55 2.1K
netHg19.sql 2012-11-21 15:10 2.1K
netMm10.sql 2012-11-21 15:12 2.1K
netTarSyr2.sql 2015-05-25 09:16 2.1K
netCalJac3.sql 2012-11-21 15:09 2.1K
netGorGor3.sql 2012-11-21 14:53 2.1K
netMonDom5.sql 2012-11-21 14:58 2.1K
netPanTro4.sql 2012-11-21 14:50 2.1K
netPonAbe2.sql 2012-11-21 14:34 2.1K
all_est.sql 2012-11-21 14:34 2.1K
intronEst.sql 2012-11-21 15:10 2.1K
all_mrna.sql 2020-09-01 09:22 2.1K
xenoMrna.sql 2020-09-01 09:22 2.1K
refSeqAli.sql 2020-09-01 09:22 2.1K
xenoRefSeqAli.sql 2020-09-01 09:22 2.1K
tableList.txt.gz 2024-11-17 03:37 3.9K
tableDescriptions.txt.gz 2024-11-16 02:03 5.5K
trackDb.txt.gz 2023-03-28 13:52 34K
ctgPos2.txt.gz 2012-11-21 14:59 64K
gbLoaded.txt.gz 2020-09-01 09:22 81K
cytoBandIdeo.txt.gz 2013-04-28 21:17 113K
chromInfo.txt.gz 2012-11-21 15:09 118K
ucscToINSDC.txt.gz 2013-09-15 18:55 188K
microsat.txt.gz 2015-08-24 00:53 262K
refFlat.txt.gz 2020-09-01 09:22 526K
gold.txt.gz 2012-11-21 14:55 539K
cpgIslandExt.txt.gz 2012-11-21 15:08 546K
refGene.txt.gz 2020-09-01 09:22 571K
refSeqAli.txt.gz 2020-09-01 09:22 588K
estOrientInfo.txt.gz 2012-11-21 15:09 776K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:17 1.1M
intronEst.txt.gz 2012-11-21 15:10 2.1M
augustusGene.txt.gz 2015-07-26 17:21 2.1M
geneid.txt.gz 2015-11-22 21:02 2.6M
genscan.txt.gz 2012-11-21 15:08 2.8M
all_est.txt.gz 2012-11-21 14:34 3.5M
mrnaOrientInfo.txt.gz 2020-09-01 09:22 4.2M
gap.txt.gz 2012-11-21 14:58 5.2M
chainCalJac3.txt.gz 2012-11-21 15:09 13M
chainHg19.txt.gz 2012-11-21 15:07 15M
chainPanTro4.txt.gz 2012-11-21 14:53 15M
all_mrna.txt.gz 2020-09-01 09:22 16M
chainHg38.txt.gz 2015-05-18 07:56 16M
nestedRepeats.txt.gz 2012-11-21 15:10 17M
netMonDom5.txt.gz 2012-11-21 14:58 18M
simpleRepeat.txt.gz 2012-11-21 15:09 24M
netHg38.txt.gz 2015-05-18 07:55 26M
netHg19.txt.gz 2012-11-21 15:10 26M
netPanTro4.txt.gz 2012-11-21 14:50 28M
xenoRefFlat.txt.gz 2020-09-01 09:22 29M
xenoRefGene.txt.gz 2020-09-01 09:22 33M
xenoRefSeqAli.txt.gz 2020-09-01 09:22 34M
netPonAbe2.txt.gz 2012-11-21 14:34 36M
netGorGor3.txt.gz 2012-11-21 14:53 36M
netCalJac3.txt.gz 2012-11-21 15:09 46M
chainRn5.txt.gz 2012-11-21 14:34 49M
chainMm10.txt.gz 2012-11-21 14:45 60M
netTarSyr2.txt.gz 2015-05-25 09:16 69M
netRn5.txt.gz 2012-11-21 15:11 70M
netMm10.txt.gz 2012-11-21 15:12 70M
rmsk.txt.gz 2012-11-21 15:07 134M
windowmaskerSdust.txt.gz 2012-11-21 15:12 145M
chainPanTro4Link.txt.gz 2012-11-21 14:42 165M
chainHg19Link.txt.gz 2012-11-21 14:58 168M
chainHg38Link.txt.gz 2015-05-18 07:55 176M
chainGorGor3.txt.gz 2012-11-21 14:55 218M
chainCalJac3Link.txt.gz 2012-11-21 14:53 221M
chainPonAbe2.txt.gz 2012-11-21 14:35 266M
chainTarSyr2.txt.gz 2015-05-25 09:10 266M
xenoMrna.txt.gz 2020-09-01 09:22 323M
chainRn5Link.txt.gz 2012-11-21 14:43 447M
chainMm10Link.txt.gz 2012-11-21 14:48 474M
chainMonDom5.txt.gz 2012-11-21 14:56 539M
chainGorGor3Link.txt.gz 2012-11-21 14:51 646M
chainPonAbe2Link.txt.gz 2012-11-21 14:37 817M
chainTarSyr2Link.txt.gz 2015-05-25 09:12 1.1G
chainMonDom5Link.txt.gz 2012-11-21 15:01 1.3G