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.
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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 -
all_est.sql 10-Jul-2016 09:15 2.1K
all_est.txt.gz 10-Jul-2016 09:15 6.2M
all_mrna.sql 09-Jul-2017 12:30 2.1K
all_mrna.txt.gz 09-Jul-2017 12:30 36K
augustusGene.sql 26-Jul-2015 17:21 1.9K
augustusGene.txt.gz 26-Jul-2015 17:21 1.9M
bigFiles.sql 09-Jul-2017 12:27 1.4K
bigFiles.txt.gz 09-Jul-2017 12:27 68
chainTarSyr2.sql 25-May-2015 08:21 1.7K
chainTarSyr2.txt.gz 25-May-2015 08:21 129M
chainTarSyr2Link.sql 25-May-2015 08:16 1.5K
chainTarSyr2Link.txt.gz 25-May-2015 08:18 832M
chromInfo.sql 22-Jan-2013 13:02 1.4K
chromInfo.txt.gz 22-Jan-2013 13:02 300K
cpgIslandExt.sql 22-Jan-2013 12:58 1.7K
cpgIslandExt.txt.gz 22-Jan-2013 12:58 597K
cpgIslandExtUnmasked.sql 01-Jun-2014 18:39 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 18:39 1.7M
cytoBandIdeo.sql 28-Apr-2013 20:39 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 20:39 308K
ensGene.sql 20-Nov-2016 09:14 1.9K
ensGene.txt.gz 20-Nov-2016 09:14 2.3M
ensGtp.sql 20-Nov-2016 09:13 1.4K
ensGtp.txt.gz 20-Nov-2016 09:13 302K
ensPep.sql 20-Nov-2016 09:13 1.3K
ensPep.txt.gz 20-Nov-2016 09:13 6.4M
ensemblSource.sql 20-Nov-2016 09:14 1.4K
ensemblSource.txt.gz 20-Nov-2016 09:14 93K
ensemblToGeneName.sql 20-Nov-2016 09:16 1.4K
ensemblToGeneName.txt.gz 20-Nov-2016 09:16 158K
estOrientInfo.sql 10-Jul-2016 09:15 1.8K
estOrientInfo.txt.gz 10-Jul-2016 09:15 1.7M
gap.sql 22-Jan-2013 13:04 1.6K
gap.txt.gz 22-Jan-2013 13:04 1.7M
gbLoaded.sql 09-Jul-2017 12:30 1.6K
gbLoaded.txt.gz 09-Jul-2017 12:30 13K
gc5BaseBw.sql 22-Jan-2013 13:01 1.3K
gc5BaseBw.txt.gz 22-Jan-2013 13:01 63
geneid.sql 22-Nov-2015 20:32 1.9K
geneid.txt.gz 22-Nov-2015 20:32 2.1M
genscan.sql 22-Jan-2013 13:01 1.7K
genscan.txt.gz 22-Jan-2013 13:01 2.5M
genscanSubopt.sql 22-Jan-2013 13:01 1.6K
genscanSubopt.txt.gz 22-Jan-2013 13:01 5.9M
gold.sql 22-Jan-2013 13:02 1.7K
gold.txt.gz 22-Jan-2013 13:02 1.0M
grp.sql 02-Mar-2014 04:14 1.3K
grp.txt.gz 02-Mar-2014 04:14 208
hgFindSpec.sql 09-Jul-2017 12:30 1.7K
hgFindSpec.txt.gz 09-Jul-2017 12:30 662
history.sql 22-Jan-2013 13:01 1.6K
history.txt.gz 22-Jan-2013 13:01 375
intronEst.sql 10-Jul-2016 09:15 2.1K
intronEst.txt.gz 10-Jul-2016 09:15 3.1M
microsat.sql 24-Aug-2015 00:04 1.5K
microsat.txt.gz 24-Aug-2015 00:04 314K
mrnaOrientInfo.sql 09-Jul-2017 12:30 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 12:30 16K
nestedRepeats.sql 22-Jan-2013 12:58 1.9K
nestedRepeats.txt.gz 22-Jan-2013 12:58 18M
netTarSyr2.sql 25-May-2015 08:21 2.1K
netTarSyr2.txt.gz 25-May-2015 08:21 71M
refFlat.sql 25-Jun-2017 19:29 1.7K
refFlat.txt.gz 25-Jun-2017 19:29 41K
refGene.sql 25-Jun-2017 19:38 1.9K
refGene.txt.gz 25-Jun-2017 19:38 44K
refSeqAli.sql 13-Mar-2017 10:24 2.1K
refSeqAli.txt.gz 13-Mar-2017 10:24 47K
rmsk.sql 22-Jan-2013 12:58 1.9K
rmsk.txt.gz 22-Jan-2013 12:58 137M
simpleRepeat.sql 22-Jan-2013 12:58 1.9K
simpleRepeat.txt.gz 22-Jan-2013 12:58 29M
tableDescriptions.sql 09-Jul-2017 12:30 1.4K
tableDescriptions.txt.gz 09-Jul-2017 12:30 4.4K
tableList.sql 09-Jul-2017 12:30 1.5K
tableList.txt.gz 09-Jul-2017 12:30 2.7K
trackDb.sql 09-Jul-2017 12:30 2.0K
trackDb.txt.gz 09-Jul-2017 12:30 31K
ucscToEnsembl.sql 13-Apr-2015 05:01 1.4K
ucscToEnsembl.txt.gz 13-Apr-2015 05:01 299K
windowmaskerSdust.sql 22-Jan-2013 13:00 1.5K
windowmaskerSdust.txt.gz 22-Jan-2013 13:00 144M
xenoMrna.sql 09-Jul-2017 12:27 2.1K
xenoMrna.txt.gz 09-Jul-2017 12:28 305M
xenoRefFlat.sql 09-Jul-2017 12:30 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 12:30 27M
xenoRefGene.sql 09-Jul-2017 12:30 1.9K
xenoRefGene.txt.gz 09-Jul-2017 12:30 30M
xenoRefSeqAli.sql 09-Jul-2017 12:30 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 12:30 27M