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 -
all_est.sql 2016-04-12 13:20 2.1K
all_est.txt.gz 2016-04-12 13:20 3.4M
history.sql 2016-04-12 13:20 1.6K
history.txt.gz 2016-04-12 13:20 513
augustusGene.sql 2016-04-12 13:20 1.9K
augustusGene.txt.gz 2016-04-12 13:20 2.3M
intronEst.sql 2016-04-12 13:20 2.1K
intronEst.txt.gz 2016-04-12 13:20 2.2M
chainHg38.sql 2016-04-12 13:20 1.7K
chainHg38.txt.gz 2016-04-12 13:20 25M
chainHg38Link.sql 2016-04-12 13:20 1.5K
chainHg38Link.txt.gz 2016-04-12 13:21 211M
chainMm10.sql 2016-04-12 13:21 1.7K
microsat.sql 2016-04-12 13:21 1.5K
microsat.txt.gz 2016-04-12 13:21 399K
chainMm10.txt.gz 2016-04-12 13:21 71M
chainMm10Link.sql 2016-04-12 13:22 1.5K
chainMm10Link.txt.gz 2016-04-12 13:22 515M
chromInfo.sql 2016-04-12 13:25 1.4K
chromInfo.txt.gz 2016-04-12 13:25 1.3M
cpgIslandExt.sql 2016-04-12 13:25 1.7K
cpgIslandExt.txt.gz 2016-04-12 13:25 675K
gc5BaseBw.sql 2016-04-12 13:25 1.3K
gc5BaseBw.txt.gz 2016-04-12 13:25 66
cpgIslandExtUnmasked.sql 2016-04-12 13:26 1.7K
cpgIslandExtUnmasked.txt.gz 2016-04-12 13:26 1.8M
cytoBandIdeo.sql 2016-04-12 13:26 1.5K
cytoBandIdeo.txt.gz 2016-04-12 13:26 1.4M
genscan.sql 2016-04-12 13:26 1.7K
genscan.txt.gz 2016-04-12 13:26 3.0M
gold.sql 2016-04-12 13:26 1.7K
gold.txt.gz 2016-04-12 13:26 3.9M
estOrientInfo.sql 2016-04-12 13:26 1.8K
estOrientInfo.txt.gz 2016-04-12 13:26 791K
grp.sql 2016-04-12 13:26 1.3K
grp.txt.gz 2016-04-12 13:26 213
gap.sql 2016-04-12 13:26 1.6K
gap.txt.gz 2016-04-12 13:26 810K
nestedRepeats.sql 2016-04-12 13:26 1.9K
nestedRepeats.txt.gz 2016-04-12 13:26 18M
netHg38.sql 2016-04-12 13:28 2.1K
netHg38.txt.gz 2016-04-12 13:28 26M
netMm10.sql 2016-04-12 13:29 2.1K
netMm10.txt.gz 2016-04-12 13:29 72M
rmsk.sql 2016-04-12 13:30 1.9K
rmsk.txt.gz 2016-04-12 13:30 150M
simpleRepeat.sql 2016-04-12 13:30 1.9K
simpleRepeat.txt.gz 2016-04-12 13:30 42M
ucscToINSDC.sql 2016-04-12 13:31 1.4K
ucscToINSDC.txt.gz 2016-04-12 13:31 2.1M
windowmaskerSdust.sql 2016-04-12 13:31 1.5K
windowmaskerSdust.txt.gz 2016-04-12 13:31 151M
chainChlSab2.sql 2016-10-30 09:48 1.7K
chainChlSab2.txt.gz 2016-10-30 09:48 23M
chainChlSab2Link.sql 2016-10-30 09:48 1.5K
chainChlSab2Link.txt.gz 2016-10-30 09:48 122M
netChlSab2.sql 2016-10-30 09:48 2.1K
netChlSab2.txt.gz 2016-10-30 09:48 17M
chainRn6.sql 2017-03-28 02:24 1.7K
chainRn6.txt.gz 2017-03-28 02:31 615M
chainRn6Link.sql 2017-03-28 02:53 1.5K
chainRn6Link.txt.gz 2017-03-28 03:19 2.3G
netRn6.sql 2017-03-28 04:41 2.1K
netRn6.txt.gz 2017-03-28 04:42 79M
ncbiRefSeq.sql 2018-02-09 13:51 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:51 3.5M
ncbiRefSeqCurated.sql 2018-02-09 13:51 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:51 543K
ncbiRefSeqPredicted.sql 2018-02-09 13:51 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:51 3.2M
ncbiRefSeqLink.sql 2018-02-09 13:51 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:51 1.7M
ncbiRefSeqPsl.sql 2018-02-09 13:52 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:52 4.8M
chromAlias.sql 2018-02-18 08:25 1.4K
chromAlias.txt.gz 2018-02-18 08:25 2.9M
ucscToRefSeq.sql 2018-02-18 08:25 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:25 2.1M
extNcbiRefSeq.sql 2018-08-14 02:29 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:29 91
ncbiRefSeqCds.sql 2018-08-14 02:29 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:29 375K
ncbiRefSeqOther.sql 2018-08-14 02:29 1.3K
ncbiRefSeqOther.txt.gz 2018-08-14 02:29 75
ncbiRefSeqPepTable.sql 2018-08-14 02:29 1.4K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:29 9.3M
seqNcbiRefSeq.sql 2018-08-14 02:29 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:29 1.0M
ensGene.sql 2019-02-10 03:42 1.9K
ensGene.txt.gz 2019-02-10 03:42 3.3M
ensemblSource.sql 2019-02-10 03:42 1.4K
ensemblSource.txt.gz 2019-02-10 03:42 170K
ensPep.sql 2019-02-10 03:42 1.3K
ensPep.txt.gz 2019-02-10 03:42 12M
ensemblToGeneName.sql 2019-02-10 03:42 1.4K
ensemblToGeneName.txt.gz 2019-02-10 03:42 284K
ensGtp.sql 2019-02-10 03:42 1.4K
ensGtp.txt.gz 2019-02-10 03:42 591K
all_mrna.sql 2020-09-01 09:22 2.1K
all_mrna.txt.gz 2020-09-01 09:22 16M
refGene.sql 2020-09-01 09:22 1.9K
refGene.txt.gz 2020-09-01 09:22 566K
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 26M
xenoRefFlat.sql 2020-09-01 09:22 1.7K
xenoRefFlat.txt.gz 2020-09-01 09:22 24M
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 574K
xenoRefSeqAli.sql 2020-09-01 09:22 2.1K
xenoRefSeqAli.txt.gz 2020-09-01 09:22 26M
gbLoaded.sql 2020-09-01 09:22 1.6K
gbLoaded.txt.gz 2020-09-01 09:22 44K
trackDb.sql 2023-12-05 13:50 2.1K
trackDb.txt.gz 2023-12-05 13:50 34K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:50 34K
hgFindSpec.sql 2023-12-05 13:50 1.8K
hgFindSpec.txt.gz 2023-12-05 13:50 1.3K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.3K
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 7.7K
tableList.sql 2024-04-14 03:07 1.6K
tableList.txt.gz 2024-04-14 03:07 3.8K
bigFiles.sql 2024-04-14 03:07 1.4K
bigFiles.txt.gz 2024-04-14 03:07 95