This directory contains a dump of the UCSC genome annotation database for the
Oct. 2014 (Rrox_v1/rhiRox1) assembly of the golden snub-nosed monkey genome
(rhiRox1, Novogene) .
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/7996
http://www.ncbi.nlm.nih.gov/genome/assembly/218671
http://www.ncbi.nlm.nih.gov/bioproject/266995
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=rhiRox1
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/rhiRox1/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/rhiRox1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/rhiRox1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rhiRox1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rhiRox1/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 rhiRox1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rhiRox1 --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.
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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 -
gbWarn.txt.gz 2017-03-06 11:00 31
imageClone.txt.gz 2017-03-06 10:47 35
sex.txt.gz 2017-03-06 13:01 39
cell.txt.gz 2017-03-06 10:47 40
library.txt.gz 2017-03-06 10:47 43
development.txt.gz 2017-03-06 12:47 63
gc5BaseBw.txt.gz 2017-03-06 11:40 66
ncbiRefSeqOther.txt.gz 2018-08-14 02:25 75
extNcbiRefSeq.txt.gz 2018-08-14 02:25 91
bigFiles.txt.gz 2024-11-17 03:23 95
tissue.txt.gz 2017-03-06 13:02 204
grp.txt.gz 2017-03-06 12:47 213
history.txt.gz 2017-03-06 12:48 615
keyword.txt.gz 2017-03-06 10:47 709
hgFindSpec.txt.gz 2023-12-05 13:51 1.0K
gc5BaseBw.sql 2017-03-06 11:40 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:25 1.3K
gbWarn.sql 2017-03-06 11:00 1.3K
ensPep.sql 2021-05-25 14:49 1.3K
grp.sql 2017-03-06 12:47 1.3K
ncbiRefSeqCds.sql 2018-08-14 02:25 1.4K
ensemblSource.sql 2021-05-25 14:49 1.4K
bigFiles.sql 2024-11-17 03:23 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:25 1.4K
mrnaClone.txt.gz 2017-03-06 12:45 1.4K
chromInfo.sql 2017-03-06 12:45 1.4K
cds.sql 2017-03-06 10:47 1.4K
sex.sql 2017-03-06 13:01 1.4K
cell.sql 2017-03-06 10:47 1.4K
author.sql 2017-03-06 10:47 1.4K
source.sql 2017-03-06 13:02 1.4K
tissue.sql 2017-03-06 13:02 1.4K
gbExtFile.sql 2017-03-06 12:46 1.4K
keyword.sql 2017-03-06 10:47 1.4K
library.sql 2017-03-06 10:47 1.4K
geneName.sql 2017-03-06 11:51 1.4K
organism.sql 2017-03-06 12:53 1.4K
ensemblToGeneName.sql 2021-05-25 14:47 1.4K
mrnaClone.sql 2017-03-06 12:45 1.4K
description.sql 2017-03-06 12:47 1.4K
development.sql 2017-03-06 12:47 1.4K
productName.sql 2017-03-06 12:54 1.4K
chromAlias.sql 2018-02-04 09:10 1.4K
ucscToINSDC.sql 2018-02-04 09:10 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToRefSeq.sql 2018-02-04 09:11 1.4K
ensGtp.sql 2021-05-25 14:47 1.4K
gbMiscDiff.sql 2017-03-06 12:49 1.5K
extNcbiRefSeq.sql 2018-08-14 02:25 1.5K
microsat.sql 2017-03-06 10:47 1.5K
refSeqSummary.sql 2017-03-06 12:54 1.5K
imageClone.sql 2017-03-06 10:47 1.5K
windowmaskerSdust.sql 2017-03-06 13:02 1.5K
cytoBandIdeo.sql 2017-03-06 12:46 1.5K
chainHg38Link.sql 2017-03-06 11:00 1.5K
chainTarSyr2Link.sql 2017-03-06 11:51 1.5K
tableList.sql 2024-11-17 03:23 1.6K
genscanSubopt.sql 2017-03-06 12:45 1.6K
seqNcbiRefSeq.sql 2018-08-14 02:25 1.6K
history.sql 2017-03-06 12:48 1.6K
gap.sql 2017-03-06 12:47 1.6K
refSeqStatus.sql 2017-03-06 12:54 1.6K
gbLoaded.sql 2020-09-01 09:23 1.6K
gold.sql 2017-03-06 12:46 1.7K
genscan.sql 2017-03-06 12:45 1.7K
cpgIslandExt.sql 2017-03-06 12:46 1.7K
chainHg38.sql 2017-03-06 10:47 1.7K
gbSeq.sql 2017-03-06 12:53 1.7K
chainTarSyr2.sql 2017-03-06 11:40 1.7K
cpgIslandExtUnmasked.sql 2017-03-06 12:46 1.7K
refLink.sql 2017-03-06 12:46 1.7K
xenoRefFlat.sql 2020-09-01 09:23 1.7K
hgFindSpec.sql 2023-12-05 13:51 1.8K
rmsk.sql 2017-03-06 12:54 1.9K
gbStatus.sql 2017-03-06 12:53 1.9K
simpleRepeat.sql 2017-03-06 13:01 1.9K
nestedRepeats.sql 2017-03-06 12:46 1.9K
augustusGene.sql 2017-03-06 10:47 1.9K
ensGene.sql 2021-05-25 14:47 1.9K
ncbiRefSeq.sql 2018-02-09 13:46 2.0K
xenoRefGene.sql 2020-09-01 09:23 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:47 2.0K
ncbiRefSeqLink.sql 2018-02-09 13:47 2.0K
trackDb.sql 2023-12-05 13:51 2.1K
netHg38.sql 2017-03-06 12:47 2.1K
netTarSyr2.sql 2017-03-06 12:49 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:47 2.1K
xenoRefSeqAli.sql 2020-09-01 09:23 2.1K
gbCdnaInfo.sql 2017-03-06 12:48 2.6K
tableList.txt.gz 2024-11-17 03:23 3.6K
gbMiscDiff.txt.gz 2017-03-06 12:49 4.1K
gbExtFile.txt.gz 2017-03-06 12:46 5.1K
gbLoaded.txt.gz 2020-09-01 09:23 6.6K
tableDescriptions.txt.gz 2024-11-16 02:03 7.7K
trackDb.txt.gz 2023-12-05 13:51 27K
ensemblSource.txt.gz 2021-05-25 14:49 148K
ensemblToGeneName.txt.gz 2021-05-25 14:47 218K
ncbiRefSeqCds.txt.gz 2018-08-14 02:25 243K
organism.txt.gz 2017-03-06 12:53 295K
source.txt.gz 2017-03-06 13:02 301K
microsat.txt.gz 2017-03-06 10:47 366K
cytoBandIdeo.txt.gz 2017-03-06 12:46 437K
ensGtp.txt.gz 2021-05-25 14:47 473K
chromInfo.txt.gz 2017-03-06 12:45 486K
cpgIslandExt.txt.gz 2017-03-06 12:46 584K
seqNcbiRefSeq.txt.gz 2018-08-14 02:25 631K
ucscToINSDC.txt.gz 2018-02-04 09:10 760K
ucscToRefSeq.txt.gz 2018-02-04 09:11 762K
gap.txt.gz 2017-03-06 12:47 878K
ncbiRefSeqLink.txt.gz 2018-02-09 13:47 1.1M
chromAlias.txt.gz 2018-02-04 09:10 1.3M
cpgIslandExtUnmasked.txt.gz 2017-03-06 12:46 1.5M
refSeqStatus.txt.gz 2017-03-06 12:54 1.5M
cds.txt.gz 2017-03-06 10:47 2.0M
augustusGene.txt.gz 2017-03-06 10:47 2.2M
gold.txt.gz 2017-03-06 12:46 2.3M
geneName.txt.gz 2017-03-06 11:51 2.3M
ncbiRefSeq.txt.gz 2018-02-09 13:46 2.6M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:47 2.6M
genscan.txt.gz 2017-03-06 12:45 2.8M
productName.txt.gz 2017-03-06 12:54 3.0M
ensGene.txt.gz 2021-05-25 14:47 3.0M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:47 3.1M
author.txt.gz 2017-03-06 10:47 3.5M
gbStatus.txt.gz 2017-03-06 12:54 3.6M
refSeqSummary.txt.gz 2017-03-06 12:54 4.9M
genscanSubopt.txt.gz 2017-03-06 12:45 5.8M
ensPep.txt.gz 2021-05-25 14:49 7.0M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:25 7.2M
gbCdnaInfo.txt.gz 2017-03-06 12:49 9.6M
description.txt.gz 2017-03-06 12:47 9.6M
refLink.txt.gz 2017-03-06 12:46 11M
gbSeq.txt.gz 2017-03-06 12:53 12M
nestedRepeats.txt.gz 2017-03-06 12:46 18M
netHg38.txt.gz 2017-03-06 12:48 26M
xenoRefFlat.txt.gz 2020-09-01 09:23 30M
simpleRepeat.txt.gz 2017-03-06 13:01 30M
xenoRefGene.txt.gz 2020-09-01 09:23 33M
xenoRefSeqAli.txt.gz 2020-09-01 09:23 34M
netTarSyr2.txt.gz 2017-03-06 12:51 70M
rmsk.txt.gz 2017-03-06 12:56 144M
windowmaskerSdust.txt.gz 2017-03-06 13:04 148M
chainHg38.txt.gz 2017-03-06 10:50 296M
chainTarSyr2.txt.gz 2017-03-06 11:42 309M
chainHg38Link.txt.gz 2017-03-06 11:12 900M
chainTarSyr2Link.txt.gz 2017-03-06 12:05 1.2G