This directory contains a dump of the UCSC genome annotation database for the
25 Mar-2014 (Chlorocebus_sabeus 1.1/chlSab2) assembly of the green monkey genome
(chlSab2, Vervet Genomics Consortium GCA_000409795.2) .
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/13136
http://www.ncbi.nlm.nih.gov/genome/assembly/132581
http://www.ncbi.nlm.nih.gov/bioproject/215854
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=chlSab2
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/chlSab2/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/chlSab2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/chlSab2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/chlSab2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/chlSab2/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 chlSab2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql chlSab2 --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 -
xenoRefSeqAli.txt.gz 09-Jul-2017 08:14 21M
xenoRefSeqAli.sql 09-Jul-2017 08:14 2.1K
xenoRefGene.txt.gz 09-Jul-2017 08:14 21M
xenoRefGene.sql 09-Jul-2017 08:14 1.9K
xenoRefFlat.txt.gz 09-Jul-2017 08:14 19M
xenoRefFlat.sql 09-Jul-2017 08:14 1.7K
windowmaskerSdust.txt.gz 16-Oct-2016 05:45 147M
windowmaskerSdust.sql 16-Oct-2016 05:45 1.5K
ucscToINSDC.txt.gz 16-Oct-2016 05:45 17K
ucscToINSDC.sql 16-Oct-2016 05:45 1.4K
trackDb.txt.gz 16-Jul-2017 05:33 29K
trackDb.sql 16-Jul-2017 05:33 2.0K
tableList.txt.gz 16-Jul-2017 05:33 2.6K
tableList.sql 16-Jul-2017 05:33 1.5K
tableDescriptions.txt.gz 16-Jul-2017 05:33 4.4K
tableDescriptions.sql 16-Jul-2017 05:33 1.4K
simpleRepeat.txt.gz 16-Oct-2016 05:44 26M
simpleRepeat.sql 16-Oct-2016 05:44 1.9K
rmsk.txt.gz 16-Oct-2016 05:44 135M
rmsk.sql 16-Oct-2016 05:44 1.9K
netTarSyr2.txt.gz 16-Oct-2016 05:43 68M
netTarSyr2.sql 16-Oct-2016 05:43 2.1K
netRheMac8.txt.gz 16-Oct-2016 05:43 14M
netRheMac8.sql 16-Oct-2016 05:43 2.1K
netHg38.txt.gz 16-Oct-2016 05:43 23M
netHg38.sql 16-Oct-2016 05:43 2.1K
nestedRepeats.txt.gz 16-Oct-2016 05:43 17M
nestedRepeats.sql 16-Oct-2016 05:43 1.9K
mrnaOrientInfo.txt.gz 28-May-2017 05:59 7.6K
mrnaOrientInfo.sql 28-May-2017 05:59 1.8K
microsat.txt.gz 16-Oct-2016 05:43 332K
microsat.sql 16-Oct-2016 05:43 1.5K
intronEst.txt.gz 16-Oct-2016 05:43 1.0M
intronEst.sql 16-Oct-2016 05:43 2.1K
history.txt.gz 16-Oct-2016 05:43 1.1K
history.sql 16-Oct-2016 05:43 1.6K
hgFindSpec.txt.gz 16-Jul-2017 05:33 691
hgFindSpec.sql 16-Jul-2017 05:33 1.7K
grp.txt.gz 16-Oct-2016 05:43 205
grp.sql 16-Oct-2016 05:43 1.3K
gold.txt.gz 16-Oct-2016 05:43 2.7M
gold.sql 16-Oct-2016 05:43 1.7K
genscan.txt.gz 16-Oct-2016 05:43 2.8M
genscan.sql 16-Oct-2016 05:43 1.7K
gc5BaseBw.txt.gz 16-Oct-2016 05:43 66
gc5BaseBw.sql 16-Oct-2016 05:43 1.3K
gbLoaded.txt.gz 09-Jul-2017 08:14 11K
gbLoaded.sql 09-Jul-2017 08:14 1.6K
gap.txt.gz 16-Oct-2016 05:43 1.7M
gap.sql 16-Oct-2016 05:43 1.6K
estOrientInfo.txt.gz 16-Oct-2016 05:43 456K
estOrientInfo.sql 16-Oct-2016 05:43 1.8K
ensemblToGeneName.txt.gz 12-Mar-2017 13:31 150K
ensemblToGeneName.sql 12-Mar-2017 13:31 1.4K
ensemblSource.txt.gz 12-Mar-2017 13:31 74K
ensemblSource.sql 12-Mar-2017 13:31 1.4K
ensPep.txt.gz 16-Jul-2017 05:33 5.9M
ensPep.sql 16-Jul-2017 05:33 1.3K
ensGtp.txt.gz 12-Mar-2017 13:31 248K
ensGtp.sql 12-Mar-2017 13:31 1.4K
ensGene.txt.gz 12-Mar-2017 13:31 2.1M
ensGene.sql 12-Mar-2017 13:31 1.9K
cytoBandIdeo.txt.gz 16-Oct-2016 05:43 12K
cytoBandIdeo.sql 16-Oct-2016 05:43 1.5K
cpgIslandExtUnmasked.txt.gz 16-Oct-2016 05:43 1.0M
cpgIslandExtUnmasked.sql 16-Oct-2016 05:43 1.7K
cpgIslandExt.txt.gz 16-Oct-2016 05:43 591K
cpgIslandExt.sql 16-Oct-2016 05:43 1.7K
chromInfo.txt.gz 16-Oct-2016 05:43 13K
chromInfo.sql 16-Oct-2016 05:43 1.4K
chainTarSyr2Link.txt.gz 16-Oct-2016 05:38 1.1G
chainTarSyr2Link.sql 16-Oct-2016 05:36 1.5K
chainTarSyr2.txt.gz 16-Oct-2016 05:35 285M
chainTarSyr2.sql 16-Oct-2016 05:35 1.7K
chainRheMac8Link.txt.gz 16-Oct-2016 05:34 121M
chainRheMac8Link.sql 16-Oct-2016 05:34 1.5K
chainRheMac8.txt.gz 16-Oct-2016 05:34 23M
chainRheMac8.sql 16-Oct-2016 05:34 1.7K
chainHg38Link.txt.gz 16-Oct-2016 05:33 186M
chainHg38Link.sql 16-Oct-2016 05:33 1.5K
chainHg38.txt.gz 16-Oct-2016 05:33 17M
chainHg38.sql 16-Oct-2016 05:33 1.7K
bigFiles.txt.gz 16-Jul-2017 05:33 69
bigFiles.sql 16-Jul-2017 05:33 1.4K
augustusGene.txt.gz 16-Oct-2016 05:33 2.2M
augustusGene.sql 16-Oct-2016 05:33 1.9K
all_mrna.txt.gz 28-May-2017 05:59 36K
all_mrna.sql 28-May-2017 05:59 2.1K
all_est.txt.gz 16-Oct-2016 05:33 1.4M
all_est.sql 16-Oct-2016 05:33 2.1K