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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
bigFiles.txt.gz 2024-11-24 03:14 95
bigFiles.sql 2024-11-24 03:14 1.4K
tableList.txt.gz 2024-11-24 03:14 3.6K
tableList.sql 2024-11-24 03:14 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 7.7K
tableDescriptions.sql 2024-11-23 02:03 1.4K
hgFindSpec.txt.gz 2023-12-05 13:51 1.0K
hgFindSpec.sql 2023-12-05 13:51 1.8K
trackDb.txt.gz 2023-12-05 13:51 27K
trackDb.sql 2023-12-05 13:51 2.1K
ensPep.txt.gz 2021-05-25 14:49 7.0M
ensPep.sql 2021-05-25 14:49 1.3K
ensemblSource.txt.gz 2021-05-25 14:49 148K
ensemblSource.sql 2021-05-25 14:49 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:47 218K
ensemblToGeneName.sql 2021-05-25 14:47 1.4K
ensGtp.txt.gz 2021-05-25 14:47 473K
ensGtp.sql 2021-05-25 14:47 1.4K
ensGene.txt.gz 2021-05-25 14:47 3.0M
ensGene.sql 2021-05-25 14:47 1.9K
gbLoaded.txt.gz 2020-09-01 09:23 6.6K
gbLoaded.sql 2020-09-01 09:23 1.6K
xenoRefSeqAli.txt.gz 2020-09-01 09:23 34M
xenoRefSeqAli.sql 2020-09-01 09:23 2.1K
xenoRefFlat.txt.gz 2020-09-01 09:23 30M
xenoRefFlat.sql 2020-09-01 09:23 1.7K
xenoRefGene.txt.gz 2020-09-01 09:23 33M
xenoRefGene.sql 2020-09-01 09:23 2.0K
seqNcbiRefSeq.txt.gz 2018-08-14 02:25 631K
seqNcbiRefSeq.sql 2018-08-14 02:25 1.6K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:25 7.2M
ncbiRefSeqPepTable.sql 2018-08-14 02:25 1.4K
ncbiRefSeqOther.txt.gz 2018-08-14 02:25 75
ncbiRefSeqOther.sql 2018-08-14 02:25 1.3K
ncbiRefSeqCds.txt.gz 2018-08-14 02:25 243K
ncbiRefSeqCds.sql 2018-08-14 02:25 1.4K
extNcbiRefSeq.txt.gz 2018-08-14 02:25 91
extNcbiRefSeq.sql 2018-08-14 02:25 1.5K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:47 3.1M
ncbiRefSeqPsl.sql 2018-02-09 13:47 2.1K
ncbiRefSeqLink.txt.gz 2018-02-09 13:47 1.1M
ncbiRefSeqLink.sql 2018-02-09 13:47 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:47 2.6M
ncbiRefSeqPredicted.sql 2018-02-09 13:47 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:46 2.6M
ncbiRefSeq.sql 2018-02-09 13:46 2.0K
ucscToRefSeq.txt.gz 2018-02-04 09:11 762K
ucscToRefSeq.sql 2018-02-04 09:11 1.4K
ucscToINSDC.txt.gz 2018-02-04 09:10 760K
ucscToINSDC.sql 2018-02-04 09:10 1.4K
chromAlias.txt.gz 2018-02-04 09:10 1.3M
chromAlias.sql 2018-02-04 09:10 1.4K
windowmaskerSdust.txt.gz 2017-03-06 13:04 148M
windowmaskerSdust.sql 2017-03-06 13:02 1.5K
tissue.txt.gz 2017-03-06 13:02 204
tissue.sql 2017-03-06 13:02 1.4K
source.txt.gz 2017-03-06 13:02 301K
source.sql 2017-03-06 13:02 1.4K
simpleRepeat.txt.gz 2017-03-06 13:01 30M
simpleRepeat.sql 2017-03-06 13:01 1.9K
sex.txt.gz 2017-03-06 13:01 39
sex.sql 2017-03-06 13:01 1.4K
rmsk.txt.gz 2017-03-06 12:56 144M
rmsk.sql 2017-03-06 12:54 1.9K
refSeqSummary.txt.gz 2017-03-06 12:54 4.9M
refSeqSummary.sql 2017-03-06 12:54 1.5K
refSeqStatus.txt.gz 2017-03-06 12:54 1.5M
refSeqStatus.sql 2017-03-06 12:54 1.6K
productName.txt.gz 2017-03-06 12:54 3.0M
productName.sql 2017-03-06 12:54 1.4K
gbStatus.txt.gz 2017-03-06 12:54 3.6M
organism.txt.gz 2017-03-06 12:53 295K
organism.sql 2017-03-06 12:53 1.4K
gbStatus.sql 2017-03-06 12:53 1.9K
gbSeq.txt.gz 2017-03-06 12:53 12M
gbSeq.sql 2017-03-06 12:53 1.7K
netTarSyr2.txt.gz 2017-03-06 12:51 70M
netTarSyr2.sql 2017-03-06 12:49 2.1K
gbMiscDiff.txt.gz 2017-03-06 12:49 4.1K
gbMiscDiff.sql 2017-03-06 12:49 1.5K
gbCdnaInfo.txt.gz 2017-03-06 12:49 9.6M
history.txt.gz 2017-03-06 12:48 615
history.sql 2017-03-06 12:48 1.6K
gbCdnaInfo.sql 2017-03-06 12:48 2.6K
netHg38.txt.gz 2017-03-06 12:48 26M
netHg38.sql 2017-03-06 12:47 2.1K
gap.txt.gz 2017-03-06 12:47 878K
gap.sql 2017-03-06 12:47 1.6K
development.txt.gz 2017-03-06 12:47 63
development.sql 2017-03-06 12:47 1.4K
description.txt.gz 2017-03-06 12:47 9.6M
grp.txt.gz 2017-03-06 12:47 213
grp.sql 2017-03-06 12:47 1.3K
description.sql 2017-03-06 12:47 1.4K
nestedRepeats.txt.gz 2017-03-06 12:46 18M
nestedRepeats.sql 2017-03-06 12:46 1.9K
cytoBandIdeo.txt.gz 2017-03-06 12:46 437K
cytoBandIdeo.sql 2017-03-06 12:46 1.5K
gold.txt.gz 2017-03-06 12:46 2.3M
gold.sql 2017-03-06 12:46 1.7K
cpgIslandExtUnmasked.txt.gz 2017-03-06 12:46 1.5M
gbExtFile.txt.gz 2017-03-06 12:46 5.1K
gbExtFile.sql 2017-03-06 12:46 1.4K
cpgIslandExtUnmasked.sql 2017-03-06 12:46 1.7K
refLink.txt.gz 2017-03-06 12:46 11M
refLink.sql 2017-03-06 12:46 1.7K
cpgIslandExt.txt.gz 2017-03-06 12:46 584K
cpgIslandExt.sql 2017-03-06 12:46 1.7K
genscanSubopt.txt.gz 2017-03-06 12:45 5.8M
genscanSubopt.sql 2017-03-06 12:45 1.6K
chromInfo.txt.gz 2017-03-06 12:45 486K
mrnaClone.txt.gz 2017-03-06 12:45 1.4K
mrnaClone.sql 2017-03-06 12:45 1.4K
chromInfo.sql 2017-03-06 12:45 1.4K
genscan.txt.gz 2017-03-06 12:45 2.8M
genscan.sql 2017-03-06 12:45 1.7K
chainTarSyr2Link.txt.gz 2017-03-06 12:05 1.2G
chainTarSyr2Link.sql 2017-03-06 11:51 1.5K
geneName.txt.gz 2017-03-06 11:51 2.3M
geneName.sql 2017-03-06 11:51 1.4K
chainTarSyr2.txt.gz 2017-03-06 11:42 309M
gc5BaseBw.txt.gz 2017-03-06 11:40 66
gc5BaseBw.sql 2017-03-06 11:40 1.3K
chainTarSyr2.sql 2017-03-06 11:40 1.7K
chainHg38Link.txt.gz 2017-03-06 11:12 900M
gbWarn.txt.gz 2017-03-06 11:00 31
gbWarn.sql 2017-03-06 11:00 1.3K
chainHg38Link.sql 2017-03-06 11:00 1.5K
chainHg38.txt.gz 2017-03-06 10:50 296M
chainHg38.sql 2017-03-06 10:47 1.7K
microsat.txt.gz 2017-03-06 10:47 366K
microsat.sql 2017-03-06 10:47 1.5K
library.txt.gz 2017-03-06 10:47 43
library.sql 2017-03-06 10:47 1.4K
cell.txt.gz 2017-03-06 10:47 40
cell.sql 2017-03-06 10:47 1.4K
cds.txt.gz 2017-03-06 10:47 2.0M
keyword.txt.gz 2017-03-06 10:47 709
keyword.sql 2017-03-06 10:47 1.4K
cds.sql 2017-03-06 10:47 1.4K
author.txt.gz 2017-03-06 10:47 3.5M
imageClone.txt.gz 2017-03-06 10:47 35
imageClone.sql 2017-03-06 10:47 1.5K
author.sql 2017-03-06 10:47 1.4K
augustusGene.txt.gz 2017-03-06 10:47 2.2M
augustusGene.sql 2017-03-06 10:47 1.9K