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 -
gap.sql 2012-11-16 12:04 1.7K
gap.txt.gz 2012-11-16 12:04 3.8M
chromInfo.sql 2012-11-16 12:04 1.4K
chromInfo.txt.gz 2012-11-16 12:04 1.6M
cpgIslandExt.sql 2012-11-16 12:07 1.7K
cpgIslandExt.txt.gz 2012-11-16 12:07 597K
simpleRepeat.sql 2012-11-16 12:07 2.1K
simpleRepeat.txt.gz 2012-11-16 12:07 25M
chainCalJac3.sql 2012-11-16 12:07 1.7K
chainCalJac3.txt.gz 2012-11-16 12:07 16M
chainMm10Link.sql 2012-11-16 12:07 1.5K
chainMm10Link.txt.gz 2012-11-16 12:08 444M
gold.sql 2012-11-16 12:11 1.8K
gold.txt.gz 2012-11-16 12:11 9.5M
quality.sql 2012-11-16 12:11 1.9K
quality.txt.gz 2012-11-16 12:11 68M
netCalJac3.sql 2012-11-16 12:13 2.1K
netCalJac3.txt.gz 2012-11-16 12:13 49M
netMm10.sql 2012-11-16 12:13 2.1K
netMm10.txt.gz 2012-11-16 12:13 70M
rmsk.sql 2012-11-16 12:13 2.1K
rmsk.txt.gz 2012-11-16 12:13 135M
chainGorGor3.sql 2012-11-16 12:14 1.7K
chainGorGor3.txt.gz 2012-11-16 12:14 19M
chainGorGor3Link.sql 2012-11-16 12:14 1.6K
chainGorGor3Link.txt.gz 2012-11-16 12:15 150M
netGorGor3.sql 2012-11-16 12:15 2.1K
netGorGor3.txt.gz 2012-11-16 12:15 33M
chainMm10.sql 2012-11-16 12:15 1.7K
chainMm10.txt.gz 2012-11-16 12:15 59M
windowmaskerSdust.sql 2012-11-16 12:16 1.5K
windowmaskerSdust.txt.gz 2012-11-16 12:16 151M
chainCalJac3Link.sql 2012-11-16 12:16 1.6K
chainCalJac3Link.txt.gz 2012-11-16 12:16 213M
gc5Base.sql 2012-11-16 12:17 1.9K
gc5Base.txt.gz 2012-11-16 12:17 19M
nestedRepeats.sql 2012-11-16 12:17 2.1K
nestedRepeats.txt.gz 2012-11-16 12:17 16M
genscan.sql 2012-11-16 12:18 1.7K
genscan.txt.gz 2012-11-16 12:18 2.8M
history.sql 2012-11-16 12:18 1.6K
history.txt.gz 2012-11-16 12:18 768
cytoBandIdeo.sql 2013-04-28 20:45 1.5K
cytoBandIdeo.txt.gz 2013-04-28 20:45 1.8M
grp.sql 2014-03-02 04:14 1.4K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 18:46 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:46 1.3M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.0M
microsat.sql 2015-08-24 00:13 1.5K
microsat.txt.gz 2015-08-24 00:13 303K
chainMacFas5.sql 2016-04-10 03:33 1.7K
chainMacFas5.txt.gz 2016-04-10 03:33 24M
chainMacFas5Link.sql 2016-04-10 03:33 1.5K
chainMacFas5Link.txt.gz 2016-04-10 03:33 84M
netMacFas5.sql 2016-04-10 03:34 2.1K
netMacFas5.txt.gz 2016-04-10 03:34 21M
all_mrna.sql 2020-03-01 08:35 2.1K
all_mrna.txt.gz 2020-03-01 08:35 33K
mrnaOrientInfo.sql 2020-05-07 00:58 1.8K
mrnaOrientInfo.txt.gz 2020-05-07 00:58 19K
refSeqAli.sql 2020-05-07 00:58 2.1K
refSeqAli.txt.gz 2020-05-07 00:58 51K
refGene.sql 2020-08-20 03:30 1.9K
refGene.txt.gz 2020-08-20 03:30 46K
refFlat.sql 2020-08-20 03:30 1.7K
refFlat.txt.gz 2020-08-20 03:30 40K
xenoRefGene.sql 2020-08-20 03:50 2.0K
xenoRefGene.txt.gz 2020-08-20 03:50 35M
xenoRefFlat.sql 2020-08-20 03:50 1.7K
xenoRefFlat.txt.gz 2020-08-20 03:50 32M
xenoRefSeqAli.sql 2020-08-20 03:50 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 03:50 39M
gbLoaded.sql 2020-08-20 03:50 1.6K
gbLoaded.txt.gz 2020-08-20 03:50 15K
trackDb.sql 2023-03-28 13:52 2.1K
trackDb.txt.gz 2023-03-28 13:52 32K
hgFindSpec.sql 2023-03-28 13:52 1.8K
hgFindSpec.txt.gz 2023-03-28 13:52 612
tableDescriptions.sql 2024-11-23 02:03 1.4K
tableDescriptions.txt.gz 2024-11-23 02:03 5.4K
tableList.sql 2024-11-24 03:06 1.6K
tableList.txt.gz 2024-11-24 03:06 2.8K
bigFiles.sql 2024-11-24 03:06 1.4K
bigFiles.txt.gz 2024-11-24 03:06 33