This directory contains a dump of the UCSC genome annotation database for
the Mar. 2012 (Baylor Panu_2.0/papAnu2) assembly of the baboon genome (papAnu2, Baylor College of Medicine).
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/394
http://www.ncbi.nlm.nih.gov/genome/assembly/383538
http://www.ncbi.nlm.nih.gov/bioproject/54005
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=papAnu2
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/papAnu2/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/papAnu2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/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 papAnu2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql papAnu2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
For conditions of use regarding the Baboon genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use
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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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
nestedRepeats.sql 2013-01-22 12:58 1.9K
nestedRepeats.txt.gz 2013-01-22 12:58 18M
cpgIslandExt.sql 2013-01-22 12:58 1.7K
cpgIslandExt.txt.gz 2013-01-22 12:58 597K
simpleRepeat.sql 2013-01-22 12:58 1.9K
simpleRepeat.txt.gz 2013-01-22 12:58 29M
rmsk.sql 2013-01-22 12:58 1.9K
rmsk.txt.gz 2013-01-22 12:58 137M
windowmaskerSdust.sql 2013-01-22 13:00 1.5K
windowmaskerSdust.txt.gz 2013-01-22 13:00 144M
history.sql 2013-01-22 13:01 1.6K
history.txt.gz 2013-01-22 13:01 375
genscan.sql 2013-01-22 13:01 1.7K
genscan.txt.gz 2013-01-22 13:01 2.5M
gc5BaseBw.sql 2013-01-22 13:01 1.3K
gc5BaseBw.txt.gz 2013-01-22 13:01 63
genscanSubopt.sql 2013-01-22 13:01 1.6K
genscanSubopt.txt.gz 2013-01-22 13:01 5.9M
gold.sql 2013-01-22 13:02 1.7K
gold.txt.gz 2013-01-22 13:02 1.0M
chromInfo.sql 2013-01-22 13:02 1.4K
chromInfo.txt.gz 2013-01-22 13:02 300K
gap.sql 2013-01-22 13:04 1.6K
gap.txt.gz 2013-01-22 13:04 1.7M
cytoBandIdeo.sql 2013-04-28 20:39 1.5K
cytoBandIdeo.txt.gz 2013-04-28 20:39 308K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 18:39 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:39 1.7M
ucscToEnsembl.sql 2015-04-13 05:01 1.4K
ucscToEnsembl.txt.gz 2015-04-13 05:01 299K
chainTarSyr2Link.sql 2015-05-25 08:16 1.5K
chainTarSyr2Link.txt.gz 2015-05-25 08:18 832M
chainTarSyr2.sql 2015-05-25 08:21 1.7K
chainTarSyr2.txt.gz 2015-05-25 08:21 129M
netTarSyr2.sql 2015-05-25 08:21 2.1K
netTarSyr2.txt.gz 2015-05-25 08:21 71M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 1.9M
microsat.sql 2015-08-24 00:04 1.5K
microsat.txt.gz 2015-08-24 00:04 314K
geneid.sql 2015-11-22 20:32 1.9K
geneid.txt.gz 2015-11-22 20:32 2.1M
estOrientInfo.sql 2016-07-10 09:15 1.8K
estOrientInfo.txt.gz 2016-07-10 09:15 1.7M
intronEst.sql 2016-07-10 09:15 2.1K
intronEst.txt.gz 2016-07-10 09:15 3.1M
all_est.sql 2016-07-10 09:15 2.1K
all_est.txt.gz 2016-07-10 09:15 6.2M
ensGtp.sql 2018-02-04 08:54 1.4K
ensPep.sql 2018-02-04 08:54 1.3K
ensPep.txt.gz 2018-02-04 08:54 6.4M
ensGtp.txt.gz 2018-02-04 08:54 302K
ensGene.sql 2018-02-04 08:56 1.9K
ensGene.txt.gz 2018-02-04 08:56 2.3M
ensemblSource.sql 2018-02-04 08:56 1.4K
ensemblSource.txt.gz 2018-02-04 08:56 93K
ensemblToGeneName.sql 2018-02-04 08:57 1.4K
ensemblToGeneName.txt.gz 2018-02-04 08:57 156K
ncbiRefSeq.sql 2018-02-09 13:46 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:46 2.5M
ncbiRefSeqCurated.sql 2018-02-09 13:46 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:46 38K
ncbiRefSeqPredicted.sql 2018-02-09 13:46 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:46 2.5M
ncbiRefSeqLink.sql 2018-02-09 13:46 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:46 964K
ncbiRefSeqPsl.sql 2018-02-09 13:46 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:46 2.8M
chromAlias.sql 2018-02-18 08:15 1.4K
chromAlias.txt.gz 2018-02-18 08:15 615K
ucscToRefSeq.sql 2018-02-18 08:15 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:15 454K
extNcbiRefSeq.sql 2018-08-14 02:21 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:21 90
ncbiRefSeqCds.sql 2018-08-14 02:21 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:21 194K
ncbiRefSeqOther.sql 2018-08-14 02:21 1.3K
ncbiRefSeqOther.txt.gz 2018-08-14 02:21 75
ncbiRefSeqPepTable.sql 2018-08-14 02:21 1.4K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:21 6.4M
seqNcbiRefSeq.sql 2018-08-14 02:21 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:21 504K
all_mrna.sql 2020-03-01 08:34 2.1K
all_mrna.txt.gz 2020-03-01 08:34 38K
mrnaOrientInfo.sql 2020-05-08 21:41 1.8K
mrnaOrientInfo.txt.gz 2020-05-08 21:41 17K
refSeqAli.sql 2020-05-08 21:41 2.1K
refSeqAli.txt.gz 2020-05-08 21:41 47K
xenoMrna.sql 2020-08-22 21:58 2.1K
xenoMrna.txt.gz 2020-08-22 21:58 344M
refGene.sql 2020-08-22 22:18 1.9K
refGene.txt.gz 2020-08-22 22:18 45K
refFlat.sql 2020-08-22 22:18 1.7K
refFlat.txt.gz 2020-08-22 22:18 41K
xenoRefGene.sql 2020-08-22 22:18 2.0K
xenoRefGene.txt.gz 2020-08-22 22:18 36M
xenoRefFlat.sql 2020-08-22 22:18 1.7K
xenoRefFlat.txt.gz 2020-08-22 22:18 33M
xenoRefSeqAli.sql 2020-08-22 22:18 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 22:18 35M
gbLoaded.sql 2020-08-22 22:18 1.6K
gbLoaded.txt.gz 2020-08-22 22:18 41K
trackDb.sql 2023-12-05 13:51 2.1K
trackDb.txt.gz 2023-12-05 13:51 31K
hgFindSpec.sql 2023-12-05 13:51 1.8K
hgFindSpec.txt.gz 2023-12-05 13:51 1.2K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
tableList.sql 2024-11-17 03:38 1.6K
tableList.txt.gz 2024-11-17 03:38 3.3K
bigFiles.sql 2024-11-17 03:38 1.4K
bigFiles.txt.gz 2024-11-17 03:38 94