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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
all_est.sql 2016-10-16 05:33 2.1K
all_est.txt.gz 2016-10-16 05:33 1.4M
augustusGene.sql 2016-10-16 05:33 1.9K
augustusGene.txt.gz 2016-10-16 05:33 2.2M
chainHg38.sql 2016-10-16 05:33 1.7K
chainHg38.txt.gz 2016-10-16 05:33 17M
chainHg38Link.sql 2016-10-16 05:33 1.5K
chainHg38Link.txt.gz 2016-10-16 05:33 186M
chainRheMac8.sql 2016-10-16 05:34 1.7K
chainRheMac8.txt.gz 2016-10-16 05:34 23M
chainRheMac8Link.sql 2016-10-16 05:34 1.5K
chainRheMac8Link.txt.gz 2016-10-16 05:34 121M
chainTarSyr2.sql 2016-10-16 05:35 1.7K
chainTarSyr2.txt.gz 2016-10-16 05:35 285M
chainTarSyr2Link.sql 2016-10-16 05:36 1.5K
chainTarSyr2Link.txt.gz 2016-10-16 05:38 1.1G
chromInfo.sql 2016-10-16 05:43 1.4K
chromInfo.txt.gz 2016-10-16 05:43 13K
cpgIslandExt.sql 2016-10-16 05:43 1.7K
cpgIslandExt.txt.gz 2016-10-16 05:43 591K
cpgIslandExtUnmasked.sql 2016-10-16 05:43 1.7K
cpgIslandExtUnmasked.txt.gz 2016-10-16 05:43 1.0M
cytoBandIdeo.sql 2016-10-16 05:43 1.5K
cytoBandIdeo.txt.gz 2016-10-16 05:43 12K
estOrientInfo.sql 2016-10-16 05:43 1.8K
estOrientInfo.txt.gz 2016-10-16 05:43 456K
gap.sql 2016-10-16 05:43 1.6K
gap.txt.gz 2016-10-16 05:43 1.7M
gc5BaseBw.sql 2016-10-16 05:43 1.3K
gc5BaseBw.txt.gz 2016-10-16 05:43 66
genscan.sql 2016-10-16 05:43 1.7K
genscan.txt.gz 2016-10-16 05:43 2.8M
gold.sql 2016-10-16 05:43 1.7K
gold.txt.gz 2016-10-16 05:43 2.7M
history.sql 2016-10-16 05:43 1.6K
history.txt.gz 2016-10-16 05:43 1.1K
intronEst.sql 2016-10-16 05:43 2.1K
intronEst.txt.gz 2016-10-16 05:43 1.0M
microsat.sql 2016-10-16 05:43 1.5K
microsat.txt.gz 2016-10-16 05:43 332K
nestedRepeats.sql 2016-10-16 05:43 1.9K
nestedRepeats.txt.gz 2016-10-16 05:43 17M
netHg38.sql 2016-10-16 05:43 2.1K
netHg38.txt.gz 2016-10-16 05:43 23M
netRheMac8.sql 2016-10-16 05:43 2.1K
netRheMac8.txt.gz 2016-10-16 05:43 14M
netTarSyr2.sql 2016-10-16 05:43 2.1K
netTarSyr2.txt.gz 2016-10-16 05:43 68M
rmsk.sql 2016-10-16 05:44 1.9K
rmsk.txt.gz 2016-10-16 05:44 135M
simpleRepeat.sql 2016-10-16 05:44 1.9K
simpleRepeat.txt.gz 2016-10-16 05:44 26M
ucscToINSDC.sql 2016-10-16 05:45 1.4K
ucscToINSDC.txt.gz 2016-10-16 05:45 17K
windowmaskerSdust.sql 2016-10-16 05:45 1.5K
windowmaskerSdust.txt.gz 2016-10-16 05:45 147M
chromAlias.sql 2018-02-18 05:48 1.4K
chromAlias.txt.gz 2018-02-18 05:48 21K
ucscToRefSeq.sql 2018-02-18 05:48 1.4K
ucscToRefSeq.txt.gz 2018-02-18 05:48 18K
mrnaOrientInfo.sql 2019-07-14 05:57 1.8K
mrnaOrientInfo.txt.gz 2019-07-14 05:57 7.8K
all_mrna.sql 2019-07-14 05:58 2.1K
all_mrna.txt.gz 2019-07-14 05:58 37K
xenoRefGene.sql 2020-08-18 17:40 2.0K
xenoRefGene.txt.gz 2020-08-18 17:40 27M
xenoRefFlat.sql 2020-08-18 17:40 1.7K
xenoRefFlat.txt.gz 2020-08-18 17:40 24M
xenoRefSeqAli.sql 2020-08-18 17:40 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 17:40 27M
gbLoaded.sql 2020-08-18 17:40 1.6K
gbLoaded.txt.gz 2020-08-18 17:40 38K
ncbiRefSeq.sql 2021-02-10 15:47 2.0K
ncbiRefSeq.txt.gz 2021-02-10 15:47 3.7M
ncbiRefSeqCurated.sql 2021-02-10 15:47 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:47 322
ncbiRefSeqPredicted.sql 2021-02-10 15:48 2.0K
ncbiRefSeqPredicted.txt.gz 2021-02-10 15:48 3.7M
ncbiRefSeqLink.sql 2021-02-10 15:48 2.0K
ncbiRefSeqLink.txt.gz 2021-02-10 15:48 1.7M
ncbiRefSeqPsl.sql 2021-02-10 15:48 2.1K
ncbiRefSeqPsl.txt.gz 2021-02-10 15:48 5.2M
ncbiRefSeqOther.sql 2021-02-10 16:10 1.3K
ncbiRefSeqOther.txt.gz 2021-02-10 16:10 75
ncbiRefSeqCds.sql 2021-02-10 16:10 1.4K
ncbiRefSeqCds.txt.gz 2021-02-10 16:10 419K
ncbiRefSeqPepTable.sql 2021-02-10 16:10 1.4K
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:10 8.4M
extNcbiRefSeq.sql 2021-02-10 16:10 1.5K
extNcbiRefSeq.txt.gz 2021-02-10 16:10 91
seqNcbiRefSeq.sql 2021-02-10 16:10 1.6K
seqNcbiRefSeq.txt.gz 2021-02-10 16:10 1.1M
ensGene.sql 2021-05-25 14:25 1.9K
ensGene.txt.gz 2021-05-25 14:25 2.1M
ensGtp.sql 2021-05-25 14:25 1.4K
ensGtp.txt.gz 2021-05-25 14:25 240K
ensemblToGeneName.sql 2021-05-25 14:25 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:25 138K
ensemblSource.sql 2021-05-25 14:25 1.4K
ensemblSource.txt.gz 2021-05-25 14:25 74K
ensPep.sql 2021-05-25 14:25 1.3K
ensPep.txt.gz 2021-05-25 14:25 5.9M
grp.sql 2021-06-08 09:45 1.4K
grp.txt.gz 2021-06-08 09:45 200
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 68K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.2K
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.3K
tableList.sql 2024-12-08 03:16 1.6K
tableList.txt.gz 2024-12-08 03:16 3.2K
bigFiles.sql 2024-12-08 03:16 1.4K
bigFiles.txt.gz 2024-12-08 03:16 95