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 -
gc5BaseBw.txt.gz 2016-10-16 05:43 66
ncbiRefSeqOther.txt.gz 2021-02-10 16:10 75
extNcbiRefSeq.txt.gz 2021-02-10 16:10 91
bigFiles.txt.gz 2024-11-17 03:23 95
grp.txt.gz 2021-06-08 09:45 200
ncbiRefSeqCurated.txt.gz 2021-02-10 15:47 322
history.txt.gz 2016-10-16 05:43 1.1K
hgFindSpec.txt.gz 2024-07-25 09:34 1.2K
gc5BaseBw.sql 2016-10-16 05:43 1.3K
ncbiRefSeqOther.sql 2021-02-10 16:10 1.3K
ensPep.sql 2021-05-25 14:25 1.3K
ncbiRefSeqCds.sql 2021-02-10 16:10 1.4K
grp.sql 2021-06-08 09:45 1.4K
ensemblSource.sql 2021-05-25 14:25 1.4K
bigFiles.sql 2024-11-17 03:23 1.4K
ncbiRefSeqPepTable.sql 2021-02-10 16:10 1.4K
chromInfo.sql 2016-10-16 05:43 1.4K
ensemblToGeneName.sql 2021-05-25 14:25 1.4K
chromAlias.sql 2018-02-18 05:48 1.4K
ucscToINSDC.sql 2016-10-16 05:45 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToRefSeq.sql 2018-02-18 05:48 1.4K
ensGtp.sql 2021-05-25 14:25 1.4K
extNcbiRefSeq.sql 2021-02-10 16:10 1.5K
microsat.sql 2016-10-16 05:43 1.5K
windowmaskerSdust.sql 2016-10-16 05:45 1.5K
cytoBandIdeo.sql 2016-10-16 05:43 1.5K
chainHg38Link.sql 2016-10-16 05:33 1.5K
chainRheMac8Link.sql 2016-10-16 05:34 1.5K
chainTarSyr2Link.sql 2016-10-16 05:36 1.5K
tableList.sql 2024-11-17 03:23 1.6K
seqNcbiRefSeq.sql 2021-02-10 16:10 1.6K
history.sql 2016-10-16 05:43 1.6K
gap.sql 2016-10-16 05:43 1.6K
gbLoaded.sql 2020-08-18 17:40 1.6K
gold.sql 2016-10-16 05:43 1.7K
genscan.sql 2016-10-16 05:43 1.7K
cpgIslandExt.sql 2016-10-16 05:43 1.7K
chainHg38.sql 2016-10-16 05:33 1.7K
chainRheMac8.sql 2016-10-16 05:34 1.7K
chainTarSyr2.sql 2016-10-16 05:35 1.7K
cpgIslandExtUnmasked.sql 2016-10-16 05:43 1.7K
xenoRefFlat.sql 2020-08-18 17:40 1.7K
hgFindSpec.sql 2024-07-25 09:34 1.8K
estOrientInfo.sql 2016-10-16 05:43 1.8K
mrnaOrientInfo.sql 2019-07-14 05:57 1.8K
rmsk.sql 2016-10-16 05:44 1.9K
simpleRepeat.sql 2016-10-16 05:44 1.9K
nestedRepeats.sql 2016-10-16 05:43 1.9K
augustusGene.sql 2016-10-16 05:33 1.9K
ensGene.sql 2021-05-25 14:25 1.9K
ncbiRefSeq.sql 2021-02-10 15:47 2.0K
xenoRefGene.sql 2020-08-18 17:40 2.0K
ncbiRefSeqCurated.sql 2021-02-10 15:47 2.0K
ncbiRefSeqPredicted.sql 2021-02-10 15:48 2.0K
ncbiRefSeqLink.sql 2021-02-10 15:48 2.0K
trackDb.sql 2024-07-25 09:34 2.1K
netHg38.sql 2016-10-16 05:43 2.1K
netRheMac8.sql 2016-10-16 05:43 2.1K
netTarSyr2.sql 2016-10-16 05:43 2.1K
all_est.sql 2016-10-16 05:33 2.1K
all_mrna.sql 2019-07-14 05:58 2.1K
intronEst.sql 2016-10-16 05:43 2.1K
ncbiRefSeqPsl.sql 2021-02-10 15:48 2.1K
xenoRefSeqAli.sql 2020-08-18 17:40 2.1K
tableList.txt.gz 2024-11-17 03:23 3.2K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
mrnaOrientInfo.txt.gz 2019-07-14 05:57 7.8K
cytoBandIdeo.txt.gz 2016-10-16 05:43 12K
chromInfo.txt.gz 2016-10-16 05:43 13K
ucscToINSDC.txt.gz 2016-10-16 05:45 17K
ucscToRefSeq.txt.gz 2018-02-18 05:48 18K
chromAlias.txt.gz 2018-02-18 05:48 21K
all_mrna.txt.gz 2019-07-14 05:58 37K
gbLoaded.txt.gz 2020-08-18 17:40 38K
trackDb.txt.gz 2024-07-25 09:34 68K
ensemblSource.txt.gz 2021-05-25 14:25 74K
ensemblToGeneName.txt.gz 2021-05-25 14:25 138K
ensGtp.txt.gz 2021-05-25 14:25 240K
microsat.txt.gz 2016-10-16 05:43 332K
ncbiRefSeqCds.txt.gz 2021-02-10 16:10 419K
estOrientInfo.txt.gz 2016-10-16 05:43 456K
cpgIslandExt.txt.gz 2016-10-16 05:43 591K
intronEst.txt.gz 2016-10-16 05:43 1.0M
cpgIslandExtUnmasked.txt.gz 2016-10-16 05:43 1.0M
seqNcbiRefSeq.txt.gz 2021-02-10 16:10 1.1M
all_est.txt.gz 2016-10-16 05:33 1.4M
gap.txt.gz 2016-10-16 05:43 1.7M
ncbiRefSeqLink.txt.gz 2021-02-10 15:48 1.7M
ensGene.txt.gz 2021-05-25 14:25 2.1M
augustusGene.txt.gz 2016-10-16 05:33 2.2M
gold.txt.gz 2016-10-16 05:43 2.7M
genscan.txt.gz 2016-10-16 05:43 2.8M
ncbiRefSeqPredicted.txt.gz 2021-02-10 15:48 3.7M
ncbiRefSeq.txt.gz 2021-02-10 15:47 3.7M
ncbiRefSeqPsl.txt.gz 2021-02-10 15:48 5.2M
ensPep.txt.gz 2021-05-25 14:25 5.9M
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:10 8.4M
netRheMac8.txt.gz 2016-10-16 05:43 14M
chainHg38.txt.gz 2016-10-16 05:33 17M
nestedRepeats.txt.gz 2016-10-16 05:43 17M
netHg38.txt.gz 2016-10-16 05:43 23M
chainRheMac8.txt.gz 2016-10-16 05:34 23M
xenoRefFlat.txt.gz 2020-08-18 17:40 24M
simpleRepeat.txt.gz 2016-10-16 05:44 26M
xenoRefGene.txt.gz 2020-08-18 17:40 27M
xenoRefSeqAli.txt.gz 2020-08-18 17:40 27M
netTarSyr2.txt.gz 2016-10-16 05:43 68M
chainRheMac8Link.txt.gz 2016-10-16 05:34 121M
rmsk.txt.gz 2016-10-16 05:44 135M
windowmaskerSdust.txt.gz 2016-10-16 05:45 147M
chainHg38Link.txt.gz 2016-10-16 05:33 186M
chainTarSyr2.txt.gz 2016-10-16 05:35 285M
chainTarSyr2Link.txt.gz 2016-10-16 05:38 1.1G