This directory contains a dump of the UCSC genome annotation database for the
Nov. 2015 (BCM Mmul_8.0.1/rheMac8) assembly of the rhesus genome
(rheMac8, Baylor College of Medicine Genome Sequencing Center) .
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/2715158
http://www.ncbi.nlm.nih.gov/bioproject/12537
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=rheMac8
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/rheMac8/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/rheMac8/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/rheMac8/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac8/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac8/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 rheMac8 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rheMac8 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
For conditions of use regarding the Rhesus genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use
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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 -
chainRn6Link.txt.gz 2017-03-28 03:19 2.3G
chainRn6.txt.gz 2017-03-28 02:31 615M
chainMm10Link.txt.gz 2016-04-12 13:22 515M
chainHg38Link.txt.gz 2016-04-12 13:21 211M
windowmaskerSdust.txt.gz 2016-04-12 13:31 151M
rmsk.txt.gz 2016-04-12 13:30 150M
chainChlSab2Link.txt.gz 2016-10-30 09:48 122M
netRn6.txt.gz 2017-03-28 04:42 79M
netMm10.txt.gz 2016-04-12 13:29 72M
chainMm10.txt.gz 2016-04-12 13:21 71M
simpleRepeat.txt.gz 2016-04-12 13:30 42M
xenoRefSeqAli.txt.gz 2020-09-01 09:22 26M
xenoRefGene.txt.gz 2020-09-01 09:22 26M
netHg38.txt.gz 2016-04-12 13:28 26M
chainHg38.txt.gz 2016-04-12 13:20 25M
xenoRefFlat.txt.gz 2020-09-01 09:22 24M
chainChlSab2.txt.gz 2016-10-30 09:48 23M
nestedRepeats.txt.gz 2016-04-12 13:26 18M
netChlSab2.txt.gz 2016-10-30 09:48 17M
all_mrna.txt.gz 2020-09-01 09:22 16M
ensPep.txt.gz 2019-02-10 03:42 12M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:29 9.3M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:52 4.8M
mrnaOrientInfo.txt.gz 2020-09-01 09:22 4.2M
gold.txt.gz 2016-04-12 13:26 3.9M
ncbiRefSeq.txt.gz 2018-02-09 13:51 3.5M
all_est.txt.gz 2016-04-12 13:20 3.4M
ensGene.txt.gz 2019-02-10 03:42 3.3M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:51 3.2M
genscan.txt.gz 2016-04-12 13:26 3.0M
chromAlias.txt.gz 2018-02-18 08:25 2.9M
augustusGene.txt.gz 2016-04-12 13:20 2.3M
intronEst.txt.gz 2016-04-12 13:20 2.2M
ucscToRefSeq.txt.gz 2018-02-18 08:25 2.1M
ucscToINSDC.txt.gz 2016-04-12 13:31 2.1M
cpgIslandExtUnmasked.txt.gz 2016-04-12 13:26 1.8M
ncbiRefSeqLink.txt.gz 2018-02-09 13:51 1.7M
cytoBandIdeo.txt.gz 2016-04-12 13:26 1.4M
chromInfo.txt.gz 2016-04-12 13:25 1.3M
seqNcbiRefSeq.txt.gz 2018-08-14 02:29 1.0M
gap.txt.gz 2016-04-12 13:26 810K
estOrientInfo.txt.gz 2016-04-12 13:26 791K
cpgIslandExt.txt.gz 2016-04-12 13:25 675K
ensGtp.txt.gz 2019-02-10 03:42 591K
refSeqAli.txt.gz 2020-09-01 09:22 574K
refGene.txt.gz 2020-09-01 09:22 566K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:51 543K
refFlat.txt.gz 2020-09-01 09:22 526K
microsat.txt.gz 2016-04-12 13:21 399K
ncbiRefSeqCds.txt.gz 2018-08-14 02:29 375K
ensemblToGeneName.txt.gz 2019-02-10 03:42 284K
ensemblSource.txt.gz 2019-02-10 03:42 170K
trackDb.txt.gz 2024-07-25 09:34 76K
gbLoaded.txt.gz 2020-09-01 09:22 44K
tableDescriptions.txt.gz 2024-11-23 02:03 7.7K
tableList.txt.gz 2024-11-24 03:06 3.6K
xenoRefSeqAli.sql 2020-09-01 09:22 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:52 2.1K
refSeqAli.sql 2020-09-01 09:22 2.1K
all_mrna.sql 2020-09-01 09:22 2.1K
intronEst.sql 2016-04-12 13:20 2.1K
all_est.sql 2016-04-12 13:20 2.1K
netChlSab2.sql 2016-10-30 09:48 2.1K
netMm10.sql 2016-04-12 13:29 2.1K
netHg38.sql 2016-04-12 13:28 2.1K
netRn6.sql 2017-03-28 04:41 2.1K
trackDb.sql 2024-07-25 09:34 2.1K
ncbiRefSeqLink.sql 2018-02-09 13:51 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:51 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:51 2.0K
xenoRefGene.sql 2020-09-01 09:22 2.0K
ncbiRefSeq.sql 2018-02-09 13:51 2.0K
refGene.sql 2020-09-01 09:22 1.9K
augustusGene.sql 2016-04-12 13:20 1.9K
nestedRepeats.sql 2016-04-12 13:26 1.9K
simpleRepeat.sql 2016-04-12 13:30 1.9K
ensGene.sql 2019-02-10 03:42 1.9K
rmsk.sql 2016-04-12 13:30 1.9K
mrnaOrientInfo.sql 2020-09-01 09:22 1.8K
estOrientInfo.sql 2016-04-12 13:26 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
xenoRefFlat.sql 2020-09-01 09:22 1.7K
refFlat.sql 2020-09-01 09:22 1.7K
cpgIslandExtUnmasked.sql 2016-04-12 13:26 1.7K
chainChlSab2.sql 2016-10-30 09:48 1.7K
chainMm10.sql 2016-04-12 13:21 1.7K
chainHg38.sql 2016-04-12 13:20 1.7K
chainRn6.sql 2017-03-28 02:24 1.7K
cpgIslandExt.sql 2016-04-12 13:25 1.7K
genscan.sql 2016-04-12 13:26 1.7K
gold.sql 2016-04-12 13:26 1.7K
gbLoaded.sql 2020-09-01 09:22 1.6K
gap.sql 2016-04-12 13:26 1.6K
history.sql 2016-04-12 13:20 1.6K
seqNcbiRefSeq.sql 2018-08-14 02:29 1.6K
tableList.sql 2024-11-24 03:06 1.6K
chainChlSab2Link.sql 2016-10-30 09:48 1.5K
chainMm10Link.sql 2016-04-12 13:22 1.5K
chainHg38Link.sql 2016-04-12 13:20 1.5K
chainRn6Link.sql 2017-03-28 02:53 1.5K
cytoBandIdeo.sql 2016-04-12 13:26 1.5K
windowmaskerSdust.sql 2016-04-12 13:31 1.5K
microsat.sql 2016-04-12 13:21 1.5K
extNcbiRefSeq.sql 2018-08-14 02:29 1.5K
ucscToRefSeq.sql 2018-02-18 08:25 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
ucscToINSDC.sql 2016-04-12 13:31 1.4K
chromAlias.sql 2018-02-18 08:25 1.4K
ensGtp.sql 2019-02-10 03:42 1.4K
chromInfo.sql 2016-04-12 13:25 1.4K
ensemblToGeneName.sql 2019-02-10 03:42 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:29 1.4K
bigFiles.sql 2024-11-24 03:06 1.4K
ncbiRefSeqCds.sql 2018-08-14 02:29 1.4K
ensemblSource.sql 2019-02-10 03:42 1.4K
grp.sql 2016-04-12 13:26 1.3K
ensPep.sql 2019-02-10 03:42 1.3K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:29 1.3K
gc5BaseBw.sql 2016-04-12 13:25 1.3K
history.txt.gz 2016-04-12 13:20 513
grp.txt.gz 2016-04-12 13:26 213
bigFiles.txt.gz 2024-11-24 03:06 95
extNcbiRefSeq.txt.gz 2018-08-14 02:29 91
ncbiRefSeqOther.txt.gz 2018-08-14 02:29 75
gc5BaseBw.txt.gz 2016-04-12 13:25 66