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.
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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/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;'
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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 -
chainTarSyr2Link.txt.gz 2015-05-25 08:05 1.2G
chainMm10Link.txt.gz 2012-11-21 16:08 523M
chainRn5Link.txt.gz 2014-01-26 17:26 492M
xenoMrna.txt.gz 2020-08-22 18:06 321M
chainTarSyr2.txt.gz 2015-05-25 08:02 304M
chainGorGor5Link.txt.gz 2016-10-30 09:33 174M
chainRheMac3Link.txt.gz 2012-11-21 16:18 168M
windowmaskerSdust.txt.gz 2012-11-21 16:13 151M
rmsk.txt.gz 2012-11-21 16:15 139M
chainHg19Link.txt.gz 2013-06-24 23:02 125M
chainPanPan2Link.txt.gz 2017-12-24 08:43 80M
netMm10.txt.gz 2012-11-21 16:20 73M
netRn5.txt.gz 2014-01-26 17:28 72M
netTarSyr2.txt.gz 2015-05-25 08:09 69M
chainMm10.txt.gz 2012-11-21 16:14 67M
chainRn5.txt.gz 2014-01-26 17:25 54M
chainGorGor5.txt.gz 2016-10-30 09:32 44M
xenoRefGene.txt.gz 2020-08-22 18:27 33M
xenoRefSeqAli.txt.gz 2020-08-22 18:33 31M
xenoRefFlat.txt.gz 2020-08-22 18:32 30M
netRheMac3.txt.gz 2012-11-21 16:14 29M
chainHg19.txt.gz 2013-06-24 23:02 28M
simpleRepeat.txt.gz 2012-11-21 16:07 26M
chainPanPan2.txt.gz 2017-12-24 08:43 19M
nestedRepeats.txt.gz 2012-11-21 16:14 18M
chainRheMac3.txt.gz 2012-11-21 16:10 15M
netGorGor5.txt.gz 2016-10-30 09:33 11M
netPanPan2.txt.gz 2017-12-24 08:43 11M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:23 10M
netHg19.txt.gz 2013-06-24 23:02 10M
ensPep.txt.gz 2018-02-04 08:51 5.9M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.7M
ncbiRefSeq.txt.gz 2018-02-09 13:49 3.5M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.4M
genscan.txt.gz 2012-11-21 16:14 2.9M
geneid.txt.gz 2015-11-22 20:24 2.6M
gap.txt.gz 2012-11-21 16:08 2.3M
ensGene.txt.gz 2018-02-04 08:51 2.3M
augustusGene.txt.gz 2015-07-26 17:21 2.2M
ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.9M
seqNcbiRefSeq.txt.gz 2018-08-14 02:23 1.0M
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:33 1.0M
all_est.txt.gz 2016-07-10 09:12 875K
intronEst.txt.gz 2016-07-10 09:13 677K
cpgIslandExt.txt.gz 2012-11-21 16:07 627K
gold.txt.gz 2012-11-21 16:08 607K
ncbiRefSeqCds.txt.gz 2018-08-14 02:23 391K
microsat.txt.gz 2015-08-23 23:56 350K
all_mrna.txt.gz 2020-05-08 18:29 303K
ensGtp.txt.gz 2018-02-04 08:51 282K
chromAlias.txt.gz 2018-02-18 08:11 266K
refSeqAli.txt.gz 2020-08-22 18:33 225K
estOrientInfo.txt.gz 2016-07-10 09:13 221K
refGene.txt.gz 2020-08-22 18:27 219K
refFlat.txt.gz 2020-08-22 18:27 201K
ucscToRefSeq.txt.gz 2018-02-18 08:11 198K
ucscToINSDC.txt.gz 2013-09-15 18:11 192K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 192K
ucscToEnsembl.txt.gz 2012-11-21 16:16 156K
ensemblToGeneName.txt.gz 2018-02-04 08:52 140K
chromInfo.txt.gz 2012-11-21 16:08 139K
cytoBandIdeo.txt.gz 2013-04-28 20:31 133K
mrnaOrientInfo.txt.gz 2020-08-22 18:33 110K
ensemblSource.txt.gz 2018-02-04 08:51 96K
gbLoaded.txt.gz 2020-08-22 18:36 41K
trackDb_pushedout.txt.gz 2023-12-05 13:52 36K
trackDb.txt.gz 2023-12-05 13:52 36K
tableDescriptions.txt.gz 2024-04-13 02:03 6.7K
tableList.txt.gz 2024-04-14 03:35 4.3K
xenoRefSeqAli.sql 2020-08-22 18:33 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K
refSeqAli.sql 2020-08-22 18:33 2.1K
xenoMrna.sql 2020-08-22 18:06 2.1K
all_mrna.sql 2020-05-08 18:29 2.1K
intronEst.sql 2016-07-10 09:13 2.1K
all_est.sql 2016-07-10 09:12 2.1K
netRheMac3.sql 2012-11-21 16:14 2.1K
netTarSyr2.sql 2015-05-25 08:09 2.1K
netPanPan2.sql 2017-12-24 08:43 2.1K
netGorGor5.sql 2016-10-30 09:33 2.1K
netMm10.sql 2012-11-21 16:20 2.1K
netHg19.sql 2013-06-24 23:02 2.1K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
netRn5.sql 2014-01-26 17:28 2.1K
trackDb.sql 2023-12-05 13:52 2.1K
ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K
xenoRefGene.sql 2020-08-22 18:27 2.0K
ncbiRefSeq.sql 2018-02-09 13:49 2.0K
refGene.sql 2020-08-22 18:27 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
nestedRepeats.sql 2012-11-21 16:14 1.9K
simpleRepeat.sql 2012-11-21 16:07 1.9K
ensGene.sql 2018-02-04 08:51 1.9K
geneid.sql 2015-11-22 20:24 1.9K
rmsk.sql 2012-11-21 16:14 1.9K
mrnaOrientInfo.sql 2020-08-22 18:33 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
estOrientInfo.sql 2016-07-10 09:13 1.8K
hgFindSpec.sql 2023-12-05 13:52 1.8K
xenoRefFlat.sql 2020-08-22 18:32 1.7K
refFlat.sql 2020-08-22 18:27 1.7K
chainRheMac3.sql 2012-11-21 16:10 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 18:33 1.7K
chainTarSyr2.sql 2015-05-25 08:02 1.7K
chainPanPan2.sql 2017-12-24 08:43 1.7K
chainGorGor5.sql 2016-10-30 09:32 1.7K
chainMm10.sql 2012-11-21 16:14 1.7K
chainHg19.sql 2013-06-24 23:02 1.7K
chainRn5.sql 2014-01-26 17:25 1.7K
cpgIslandExt.sql 2012-11-21 16:07 1.7K
genscan.sql 2012-11-21 16:14 1.7K
gold.sql 2012-11-21 16:08 1.7K
gbLoaded.sql 2020-08-22 18:36 1.6K
gap.sql 2012-11-21 16:08 1.6K
tableList.sql 2024-04-14 03:35 1.6K
history.sql 2012-11-21 16:14 1.6K
seqNcbiRefSeq.sql 2018-08-14 02:23 1.6K
chainRheMac3Link.sql 2012-11-21 16:17 1.6K
chainTarSyr2Link.sql 2015-05-25 08:03 1.5K
chainPanPan2Link.sql 2017-12-24 08:43 1.5K
chainGorGor5Link.sql 2016-10-30 09:32 1.5K
chainMm10Link.sql 2012-11-21 16:08 1.5K
chainHg19Link.sql 2013-06-24 23:02 1.5K
chainRn5Link.sql 2014-01-26 17:25 1.5K
cytoBandIdeo.sql 2013-04-28 20:31 1.5K
windowmaskerSdust.sql 2012-11-21 16:13 1.5K
microsat.sql 2015-08-23 23:56 1.5K
extNcbiRefSeq.sql 2018-08-14 02:23 1.5K
tableDescriptions.sql 2024-04-13 02:03 1.5K
ucscToRefSeq.sql 2018-02-18 08:11 1.4K
ucscToINSDC.sql 2013-09-15 18:11 1.4K
chromAlias.sql 2018-02-18 08:11 1.4K
ensGtp.sql 2018-02-04 08:51 1.4K
bigFiles.sql 2024-04-14 03:35 1.4K
ensemblToGeneName.sql 2018-02-04 08:52 1.4K
chromInfo.sql 2012-11-21 16:08 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:23 1.4K
ncbiRefSeqCds.sql 2018-08-14 02:23 1.4K
ucscToEnsembl.sql 2012-11-21 16:16 1.4K
ensemblSource.sql 2018-02-04 08:51 1.4K
grp.sql 2014-03-02 04:14 1.3K
ensPep.sql 2018-02-04 08:51 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:23 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.3K
gc5BaseBw.sql 2012-11-21 16:21 1.3K
hgFindSpec.txt.gz 2023-12-05 13:52 1.3K
history.txt.gz 2012-11-21 16:14 647
grp.txt.gz 2014-03-02 04:14 208
bigFiles.txt.gz 2024-04-14 03:35 94
extNcbiRefSeq.txt.gz 2018-08-14 02:23 89
ncbiRefSeqOther.txt.gz 2018-08-14 02:23 75
gc5BaseBw.txt.gz 2012-11-21 16:21 63