This directory contains a dump of the UCSC genome annotation database for
the Nov. 2008 (Baylor Pham_1.0/papHam1) assembly of the baboon genome (papHam1, Baylor BCM HGSC Pham_1.0).
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/778
http://www.ncbi.nlm.nih.gov/genome/assembly/N/A
http://www.ncbi.nlm.nih.gov/bioproject/20425
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=papHam1
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/papHam1/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/papHam1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/papHam1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papHam1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papHam1/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 papHam1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql papHam1 --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.
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Name Last modified Size Description
Parent Directory -
all_mrna.sql 09-Jul-2017 12:31 2.1K
all_mrna.txt.gz 09-Jul-2017 12:31 30K
augustusGene.sql 26-Jul-2015 17:21 1.9K
augustusGene.txt.gz 26-Jul-2015 17:21 2.0M
bigFiles.sql 09-Jul-2017 12:31 1.4K
bigFiles.txt.gz 09-Jul-2017 12:31 33
chainCalJac3.sql 16-Nov-2012 12:07 1.7K
chainCalJac3.txt.gz 16-Nov-2012 12:07 16M
chainCalJac3Link.sql 16-Nov-2012 12:16 1.6K
chainCalJac3Link.txt.gz 16-Nov-2012 12:16 213M
chainGorGor3.sql 16-Nov-2012 12:14 1.7K
chainGorGor3.txt.gz 16-Nov-2012 12:14 19M
chainGorGor3Link.sql 16-Nov-2012 12:14 1.6K
chainGorGor3Link.txt.gz 16-Nov-2012 12:15 150M
chainMacFas5.sql 10-Apr-2016 03:33 1.7K
chainMacFas5.txt.gz 10-Apr-2016 03:33 24M
chainMacFas5Link.sql 10-Apr-2016 03:33 1.5K
chainMacFas5Link.txt.gz 10-Apr-2016 03:33 84M
chainMm10.sql 16-Nov-2012 12:15 1.7K
chainMm10.txt.gz 16-Nov-2012 12:15 59M
chainMm10Link.sql 16-Nov-2012 12:07 1.5K
chainMm10Link.txt.gz 16-Nov-2012 12:08 444M
chromInfo.sql 16-Nov-2012 12:04 1.4K
chromInfo.txt.gz 16-Nov-2012 12:04 1.6M
cpgIslandExt.sql 16-Nov-2012 12:07 1.7K
cpgIslandExt.txt.gz 16-Nov-2012 12:07 597K
cpgIslandExtUnmasked.sql 01-Jun-2014 18:46 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 18:46 1.3M
cytoBandIdeo.sql 28-Apr-2013 20:45 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 20:45 1.8M
gap.sql 16-Nov-2012 12:04 1.7K
gap.txt.gz 16-Nov-2012 12:04 3.8M
gbLoaded.sql 09-Jul-2017 12:31 1.6K
gbLoaded.txt.gz 09-Jul-2017 12:31 5.5K
gc5Base.sql 16-Nov-2012 12:17 1.9K
gc5Base.txt.gz 16-Nov-2012 12:17 19M
genscan.sql 16-Nov-2012 12:18 1.7K
genscan.txt.gz 16-Nov-2012 12:18 2.8M
gold.sql 16-Nov-2012 12:11 1.8K
gold.txt.gz 16-Nov-2012 12:11 9.5M
grp.sql 02-Mar-2014 04:14 1.4K
grp.txt.gz 02-Mar-2014 04:14 208
hgFindSpec.sql 28-Mar-2017 01:18 1.7K
hgFindSpec.txt.gz 28-Mar-2017 01:18 491
history.sql 16-Nov-2012 12:18 1.6K
history.txt.gz 16-Nov-2012 12:18 768
microsat.sql 24-Aug-2015 00:13 1.5K
microsat.txt.gz 24-Aug-2015 00:13 303K
mrnaOrientInfo.sql 09-Jul-2017 12:31 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 12:31 18K
nestedRepeats.sql 16-Nov-2012 12:17 2.1K
nestedRepeats.txt.gz 16-Nov-2012 12:17 16M
netCalJac3.sql 16-Nov-2012 12:13 2.1K
netCalJac3.txt.gz 16-Nov-2012 12:13 49M
netGorGor3.sql 16-Nov-2012 12:15 2.1K
netGorGor3.txt.gz 16-Nov-2012 12:15 33M
netMacFas5.sql 10-Apr-2016 03:34 2.1K
netMacFas5.txt.gz 10-Apr-2016 03:34 21M
netMm10.sql 16-Nov-2012 12:13 2.1K
netMm10.txt.gz 16-Nov-2012 12:13 70M
quality.sql 16-Nov-2012 12:11 1.9K
quality.txt.gz 16-Nov-2012 12:11 68M
refFlat.sql 25-Jun-2017 19:42 1.7K
refFlat.txt.gz 25-Jun-2017 19:42 40K
refGene.sql 25-Jun-2017 19:41 1.9K
refGene.txt.gz 25-Jun-2017 19:41 45K
refSeqAli.sql 13-Mar-2017 10:26 2.1K
refSeqAli.txt.gz 13-Mar-2017 10:26 51K
rmsk.sql 16-Nov-2012 12:13 2.1K
rmsk.txt.gz 16-Nov-2012 12:13 135M
simpleRepeat.sql 16-Nov-2012 12:07 2.1K
simpleRepeat.txt.gz 16-Nov-2012 12:07 25M
tableDescriptions.sql 09-Jul-2017 12:31 1.4K
tableDescriptions.txt.gz 09-Jul-2017 12:31 4.3K
tableList.sql 09-Jul-2017 12:31 1.5K
tableList.txt.gz 09-Jul-2017 12:31 2.8K
trackDb.sql 28-Mar-2017 01:18 2.0K
trackDb.txt.gz 28-Mar-2017 01:18 22K
windowmaskerSdust.sql 16-Nov-2012 12:16 1.5K
windowmaskerSdust.txt.gz 16-Nov-2012 12:16 151M
xenoMrna.sql 21-Feb-2016 22:26 2.1K
xenoMrna.txt.gz 21-Feb-2016 22:27 317M
xenoRefFlat.sql 09-Jul-2017 12:31 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 12:31 25M
xenoRefGene.sql 09-Jul-2017 12:30 1.9K
xenoRefGene.txt.gz 09-Jul-2017 12:31 28M
xenoRefSeqAli.sql 09-Jul-2017 12:31 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 12:31 28M