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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
simpleRepeat.sql 2012-11-21 16:07 1.9K
simpleRepeat.txt.gz 2012-11-21 16:07 26M
cpgIslandExt.sql 2012-11-21 16:07 1.7K
cpgIslandExt.txt.gz 2012-11-21 16:07 627K
gap.sql 2012-11-21 16:08 1.6K
gap.txt.gz 2012-11-21 16:08 2.3M
chromInfo.sql 2012-11-21 16:08 1.4K
chromInfo.txt.gz 2012-11-21 16:08 139K
chainMm10Link.sql 2012-11-21 16:08 1.5K
gold.sql 2012-11-21 16:08 1.7K
gold.txt.gz 2012-11-21 16:08 607K
chainMm10Link.txt.gz 2012-11-21 16:08 523M
chainRheMac3.sql 2012-11-21 16:10 1.7K
chainRheMac3.txt.gz 2012-11-21 16:10 15M
windowmaskerSdust.sql 2012-11-21 16:13 1.5K
windowmaskerSdust.txt.gz 2012-11-21 16:13 151M
genscan.sql 2012-11-21 16:14 1.7K
genscan.txt.gz 2012-11-21 16:14 2.9M
history.sql 2012-11-21 16:14 1.6K
history.txt.gz 2012-11-21 16:14 647
chainMm10.sql 2012-11-21 16:14 1.7K
chainMm10.txt.gz 2012-11-21 16:14 67M
nestedRepeats.sql 2012-11-21 16:14 1.9K
nestedRepeats.txt.gz 2012-11-21 16:14 18M
netRheMac3.sql 2012-11-21 16:14 2.1K
netRheMac3.txt.gz 2012-11-21 16:14 29M
rmsk.sql 2012-11-21 16:14 1.9K
rmsk.txt.gz 2012-11-21 16:15 139M
ucscToEnsembl.sql 2012-11-21 16:16 1.4K
ucscToEnsembl.txt.gz 2012-11-21 16:16 156K
chainRheMac3Link.sql 2012-11-21 16:17 1.6K
chainRheMac3Link.txt.gz 2012-11-21 16:18 168M
netMm10.sql 2012-11-21 16:20 2.1K
netMm10.txt.gz 2012-11-21 16:20 73M
gc5BaseBw.sql 2012-11-21 16:21 1.3K
gc5BaseBw.txt.gz 2012-11-21 16:21 63
cytoBandIdeo.sql 2013-04-28 20:31 1.5K
cytoBandIdeo.txt.gz 2013-04-28 20:31 133K
netHg19.sql 2013-06-24 23:02 2.1K
netHg19.txt.gz 2013-06-24 23:02 10M
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
ucscToINSDC.sql 2013-09-15 18:11 1.4K
ucscToINSDC.txt.gz 2013-09-15 18:11 192K
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
netRn5.sql 2014-01-26 17:28 2.1K
netRn5.txt.gz 2014-01-26 17:28 72M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 18:33 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:33 1.0M
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
netTarSyr2.sql 2015-05-25 08:09 2.1K
netTarSyr2.txt.gz 2015-05-25 08:09 69M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.2M
microsat.sql 2015-08-23 23:56 1.5K
microsat.txt.gz 2015-08-23 23:56 350K
geneid.sql 2015-11-22 20:24 1.9K
geneid.txt.gz 2015-11-22 20:24 2.6M
all_est.sql 2016-07-10 09:12 2.1K
all_est.txt.gz 2016-07-10 09:12 875K
intronEst.sql 2016-07-10 09:13 2.1K
intronEst.txt.gz 2016-07-10 09:13 677K
estOrientInfo.sql 2016-07-10 09:13 1.8K
estOrientInfo.txt.gz 2016-07-10 09:13 221K
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
netGorGor5.sql 2016-10-30 09:33 2.1K
netGorGor5.txt.gz 2016-10-30 09:33 11M
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
netPanPan2.sql 2017-12-24 08:43 2.1K
netPanPan2.txt.gz 2017-12-24 08:43 11M
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
ensemblSource.sql 2018-02-04 08:51 1.4K
ensemblSource.txt.gz 2018-02-04 08:51 96K
ensPep.sql 2018-02-04 08:51 1.3K
ensPep.txt.gz 2018-02-04 08:51 5.9M
ensemblToGeneName.sql 2018-02-04 08:52 1.4K
ensemblToGeneName.txt.gz 2018-02-04 08:52 140K
ncbiRefSeq.sql 2018-02-09 13:49 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:49 3.5M
ncbiRefSeqCurated.sql 2018-02-09 13:49 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:49 192K
ncbiRefSeqPredicted.sql 2018-02-09 13:49 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:49 3.4M
ncbiRefSeqLink.sql 2018-02-09 13:49 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:49 1.9M
ncbiRefSeqPsl.sql 2018-02-09 13:49 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:49 4.7M
chromAlias.sql 2018-02-18 08:11 1.4K
chromAlias.txt.gz 2018-02-18 08:11 266K
ucscToRefSeq.sql 2018-02-18 08:11 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:11 198K
extNcbiRefSeq.sql 2018-08-14 02:23 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:23 89
ncbiRefSeqCds.sql 2018-08-14 02:23 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:23 391K
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
seqNcbiRefSeq.sql 2018-08-14 02:23 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:23 1.0M
all_mrna.sql 2020-05-08 18:29 2.1K
all_mrna.txt.gz 2020-05-08 18:29 303K
xenoMrna.sql 2020-08-22 18:06 2.1K
xenoMrna.txt.gz 2020-08-22 18:06 321M
refGene.sql 2020-08-22 18:27 1.9K
refGene.txt.gz 2020-08-22 18:27 219K
refFlat.sql 2020-08-22 18:27 1.7K
refFlat.txt.gz 2020-08-22 18:27 201K
xenoRefGene.sql 2020-08-22 18:27 2.0K
xenoRefGene.txt.gz 2020-08-22 18:27 33M
xenoRefFlat.sql 2020-08-22 18:32 1.7K
xenoRefFlat.txt.gz 2020-08-22 18:32 30M
mrnaOrientInfo.sql 2020-08-22 18:33 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 18:33 110K
refSeqAli.sql 2020-08-22 18:33 2.1K
refSeqAli.txt.gz 2020-08-22 18:33 225K
xenoRefSeqAli.sql 2020-08-22 18:33 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 18:33 31M
gbLoaded.sql 2020-08-22 18:36 1.6K
gbLoaded.txt.gz 2020-08-22 18:36 41K
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 36K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:52 36K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.3K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.3K
tableDescriptions.sql 2024-04-20 02:03 1.5K
tableDescriptions.txt.gz 2024-04-20 02:03 6.7K
tableList.sql 2024-04-21 03:37 1.6K
tableList.txt.gz 2024-04-21 03:37 4.3K
bigFiles.sql 2024-04-21 03:37 1.4K
bigFiles.txt.gz 2024-04-21 03:37 94