This directory contains a dump of the UCSC genome annotation database for
the Feb. 2011 (CSAC 2.1.4/panTro4) assembly of the chimp genome (panTro4, CSAC Pan_troglodytes-2.1.4 (GCA_000001515.4))
from the Chimp Genome Sequencing Consortium.
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/202
http://www.ncbi.nlm.nih.gov/genome/assembly/255628
http://www.ncbi.nlm.nih.gov/bioproject/13184
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=panTro4
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
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/panTro4/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/panTro4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro4/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro4/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 panTro4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro4 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
-----------------------------------------------------------------------------
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 -
all_est.sql 2016-07-10 09:12 2.1K
all_est.txt.gz 2016-07-10 09:12 875K
all_mrna.sql 2020-05-08 18:29 2.1K
all_mrna.txt.gz 2020-05-08 18:29 303K
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.2M
bigFiles.sql 2024-12-08 03:34 1.4K
bigFiles.txt.gz 2024-12-08 03:34 94
chainGorGor5.sql 2016-10-30 09:32 1.7K
chainGorGor5.txt.gz 2016-10-30 09:32 44M
chainGorGor5Link.sql 2016-10-30 09:32 1.5K
chainGorGor5Link.txt.gz 2016-10-30 09:33 174M
chainHg19.sql 2013-06-24 23:02 1.7K
chainHg19.txt.gz 2013-06-24 23:02 28M
chainHg19Link.sql 2013-06-24 23:02 1.5K
chainHg19Link.txt.gz 2013-06-24 23:02 125M
chainMm10.sql 2012-11-21 16:14 1.7K
chainMm10.txt.gz 2012-11-21 16:14 67M
chainMm10Link.sql 2012-11-21 16:08 1.5K
chainMm10Link.txt.gz 2012-11-21 16:08 523M
chainPanPan2.sql 2017-12-24 08:43 1.7K
chainPanPan2.txt.gz 2017-12-24 08:43 19M
chainPanPan2Link.sql 2017-12-24 08:43 1.5K
chainPanPan2Link.txt.gz 2017-12-24 08:43 80M
chainRheMac3.sql 2012-11-21 16:10 1.7K
chainRheMac3.txt.gz 2012-11-21 16:10 15M
chainRheMac3Link.sql 2012-11-21 16:17 1.6K
chainRheMac3Link.txt.gz 2012-11-21 16:18 168M
chainRn5.sql 2014-01-26 17:25 1.7K
chainRn5.txt.gz 2014-01-26 17:25 54M
chainRn5Link.sql 2014-01-26 17:25 1.5K
chainRn5Link.txt.gz 2014-01-26 17:26 492M
chainTarSyr2.sql 2015-05-25 08:02 1.7K
chainTarSyr2.txt.gz 2015-05-25 08:02 304M
chainTarSyr2Link.sql 2015-05-25 08:03 1.5K
chainTarSyr2Link.txt.gz 2015-05-25 08:05 1.2G
chromAlias.sql 2018-02-18 08:11 1.4K
chromAlias.txt.gz 2018-02-18 08:11 266K
chromInfo.sql 2012-11-21 16:08 1.4K
chromInfo.txt.gz 2012-11-21 16:08 139K
cpgIslandExt.sql 2012-11-21 16:07 1.7K
cpgIslandExt.txt.gz 2012-11-21 16:07 627K
cpgIslandExtUnmasked.sql 2014-06-01 18:33 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:33 1.0M
cytoBandIdeo.sql 2013-04-28 20:31 1.5K
cytoBandIdeo.txt.gz 2013-04-28 20:31 133K
ensGene.sql 2018-02-04 08:51 1.9K
ensGene.txt.gz 2018-02-04 08:51 2.3M
ensGtp.sql 2018-02-04 08:51 1.4K
ensGtp.txt.gz 2018-02-04 08:51 282K
ensPep.sql 2018-02-04 08:51 1.3K
ensPep.txt.gz 2018-02-04 08:51 5.9M
ensemblSource.sql 2018-02-04 08:51 1.4K
ensemblSource.txt.gz 2018-02-04 08:51 96K
ensemblToGeneName.sql 2018-02-04 08:52 1.4K
ensemblToGeneName.txt.gz 2018-02-04 08:52 140K
estOrientInfo.sql 2016-07-10 09:13 1.8K
estOrientInfo.txt.gz 2016-07-10 09:13 221K
extNcbiRefSeq.sql 2018-08-14 02:23 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:23 89
gap.sql 2012-11-21 16:08 1.6K
gap.txt.gz 2012-11-21 16:08 2.3M
gbLoaded.sql 2020-08-22 18:36 1.6K
gbLoaded.txt.gz 2020-08-22 18:36 41K
gc5BaseBw.sql 2012-11-21 16:21 1.3K
gc5BaseBw.txt.gz 2012-11-21 16:21 63
geneid.sql 2015-11-22 20:24 1.9K
geneid.txt.gz 2015-11-22 20:24 2.6M
genscan.sql 2012-11-21 16:14 1.7K
genscan.txt.gz 2012-11-21 16:14 2.9M
gold.sql 2012-11-21 16:08 1.7K
gold.txt.gz 2012-11-21 16:08 607K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
history.sql 2012-11-21 16:14 1.6K
history.txt.gz 2012-11-21 16:14 647
intronEst.sql 2016-07-10 09:13 2.1K
intronEst.txt.gz 2016-07-10 09:13 677K
microsat.sql 2015-08-23 23:56 1.5K
microsat.txt.gz 2015-08-23 23:56 350K
mrnaOrientInfo.sql 2020-08-22 18:33 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 18:33 110K
ncbiRefSeq.sql 2018-02-09 13:49 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:49 3.5M
ncbiRefSeqCds.sql 2018-08-14 02:23 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:23 391K
ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 192K
ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.9M
ncbiRefSeqOther.sql 2018-08-14 02:23 1.3K
ncbiRefSeqOther.txt.gz 2018-08-14 02:23 75
ncbiRefSeqPepTable.sql 2018-08-14 02:23 1.4K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:23 10M
ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.4M
ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.7M
nestedRepeats.sql 2012-11-21 16:14 1.9K
nestedRepeats.txt.gz 2012-11-21 16:14 18M
netGorGor5.sql 2016-10-30 09:33 2.1K
netGorGor5.txt.gz 2016-10-30 09:33 11M
netHg19.sql 2013-06-24 23:02 2.1K
netHg19.txt.gz 2013-06-24 23:02 10M
netMm10.sql 2012-11-21 16:20 2.1K
netMm10.txt.gz 2012-11-21 16:20 73M
netPanPan2.sql 2017-12-24 08:43 2.1K
netPanPan2.txt.gz 2017-12-24 08:43 11M
netRheMac3.sql 2012-11-21 16:14 2.1K
netRheMac3.txt.gz 2012-11-21 16:14 29M
netRn5.sql 2014-01-26 17:28 2.1K
netRn5.txt.gz 2014-01-26 17:28 72M
netTarSyr2.sql 2015-05-25 08:09 2.1K
netTarSyr2.txt.gz 2015-05-25 08:09 69M
refFlat.sql 2020-08-22 18:27 1.7K
refFlat.txt.gz 2020-08-22 18:27 201K
refGene.sql 2020-08-22 18:27 1.9K
refGene.txt.gz 2020-08-22 18:27 219K
refSeqAli.sql 2020-08-22 18:33 2.1K
refSeqAli.txt.gz 2020-08-22 18:33 225K
rmsk.sql 2012-11-21 16:14 1.9K
rmsk.txt.gz 2012-11-21 16:15 139M
seqNcbiRefSeq.sql 2018-08-14 02:23 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:23 1.0M
simpleRepeat.sql 2012-11-21 16:07 1.9K
simpleRepeat.txt.gz 2012-11-21 16:07 26M
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.7K
tableList.sql 2024-12-08 03:34 1.6K
tableList.txt.gz 2024-12-08 03:34 4.2K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 49K
ucscToEnsembl.sql 2012-11-21 16:16 1.4K
ucscToEnsembl.txt.gz 2012-11-21 16:16 156K
ucscToINSDC.sql 2013-09-15 18:11 1.4K
ucscToINSDC.txt.gz 2013-09-15 18:11 192K
ucscToRefSeq.sql 2018-02-18 08:11 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:11 198K
windowmaskerSdust.sql 2012-11-21 16:13 1.5K
windowmaskerSdust.txt.gz 2012-11-21 16:13 151M
xenoMrna.sql 2020-08-22 18:06 2.1K
xenoMrna.txt.gz 2020-08-22 18:06 321M
xenoRefFlat.sql 2020-08-22 18:32 1.7K
xenoRefFlat.txt.gz 2020-08-22 18:32 30M
xenoRefGene.sql 2020-08-22 18:27 2.0K
xenoRefGene.txt.gz 2020-08-22 18:27 33M
xenoRefSeqAli.sql 2020-08-22 18:33 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 18:33 31M