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