This directory contains a dump of the UCSC genome annotation database for the
May 2016 (Pan_tro 3.0/panTro5) assembly of the chimp genome
(panTro5, Chimpanzee Sequencing and Analysis Consortium)
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/733711
http://www.ncbi.nlm.nih.gov/bioproject/10627
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=panTro5
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/panTro5/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/panTro5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro5/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 panTro5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro5 --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 -
all_est.sql 2016-10-14 15:36 2.1K
all_est.txt.gz 2016-10-14 15:36 889K
all_mrna.sql 2020-08-22 17:50 2.1K
all_mrna.txt.gz 2020-08-22 17:50 309K
augustusGene.sql 2016-10-14 15:36 1.9K
augustusGene.txt.gz 2016-10-14 15:36 2.4M
bigFiles.sql 2024-11-24 03:06 1.4K
bigFiles.txt.gz 2024-11-24 03:06 95
chainGorGor5.sql 2016-10-14 15:36 1.7K
chainGorGor5.txt.gz 2016-10-14 15:37 83M
chainGorGor5Link.sql 2016-10-14 15:37 1.5K
chainGorGor5Link.txt.gz 2016-10-14 15:37 253M
chainHg38.sql 2016-10-14 15:39 1.7K
chainHg38.txt.gz 2016-10-14 15:39 61M
chainHg38Link.sql 2016-10-14 15:40 1.5K
chainHg38Link.txt.gz 2016-10-14 15:40 222M
chainMm10.sql 2016-10-14 15:41 1.7K
chainMm10.txt.gz 2016-10-14 15:41 67M
chainMm10Link.sql 2016-10-14 15:41 1.5K
chainMm10Link.txt.gz 2016-10-14 15:42 542M
chainRn6.sql 2017-03-27 22:02 1.7K
chainRn6.txt.gz 2017-03-27 22:13 1.0G
chainRn6Link.sql 2017-03-27 22:47 1.5K
chainRn6Link.txt.gz 2017-03-27 23:19 3.0G
chromAlias.sql 2018-02-04 08:54 1.4K
chromAlias.txt.gz 2018-02-04 08:54 467K
chromInfo.sql 2016-10-14 15:45 1.4K
chromInfo.txt.gz 2016-10-14 15:45 218K
cpgIslandExt.sql 2016-10-14 15:45 1.7K
cpgIslandExt.txt.gz 2016-10-14 15:45 707K
cpgIslandExtUnmasked.sql 2016-10-14 15:45 1.7K
cpgIslandExtUnmasked.txt.gz 2016-10-14 15:45 1.1M
cytoBandIdeo.sql 2016-10-14 15:45 1.5K
cytoBandIdeo.txt.gz 2016-10-14 15:45 235K
ensGene.sql 2021-05-25 14:43 1.9K
ensGene.txt.gz 2021-05-25 14:43 3.5M
ensGtp.sql 2021-05-25 14:43 1.4K
ensGtp.txt.gz 2021-05-25 14:43 617K
ensPep.sql 2021-05-25 14:44 1.3K
ensPep.txt.gz 2021-05-25 14:44 15M
ensemblSource.sql 2021-05-25 14:44 1.4K
ensemblSource.txt.gz 2021-05-25 14:44 181K
ensemblToGeneName.sql 2021-05-25 14:43 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:43 310K
estOrientInfo.sql 2016-10-14 15:45 1.8K
estOrientInfo.txt.gz 2016-10-14 15:45 231K
extNcbiRefSeq.sql 2021-02-10 16:00 1.5K
extNcbiRefSeq.txt.gz 2021-02-10 16:00 91
gap.sql 2016-10-14 15:45 1.6K
gap.txt.gz 2016-10-14 15:45 364K
gbLoaded.sql 2020-08-22 18:06 1.6K
gbLoaded.txt.gz 2020-08-22 18:06 38K
gbMiscDiff.sql 2016-10-14 15:45 1.5K
gbMiscDiff.txt.gz 2016-10-14 15:45 1.2M
gc5BaseBw.sql 2016-10-14 15:46 1.3K
gc5BaseBw.txt.gz 2016-10-14 15:46 66
genscan.sql 2016-10-14 15:45 1.7K
genscan.txt.gz 2016-10-14 15:45 3.1M
gold.sql 2016-10-14 15:46 1.7K
gold.txt.gz 2016-10-14 15:46 1.1M
grp.sql 2016-10-14 15:46 1.3K
grp.txt.gz 2016-10-14 15:46 213
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
history.sql 2016-10-14 15:36 1.6K
history.txt.gz 2016-10-14 15:36 614
intronEst.sql 2016-10-14 15:37 2.1K
intronEst.txt.gz 2016-10-14 15:37 705K
microsat.sql 2016-10-14 15:40 1.5K
microsat.txt.gz 2016-10-14 15:40 347K
mrnaOrientInfo.sql 2020-08-22 17:50 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 17:50 115K
ncbiRefSeq.sql 2021-02-10 15:25 2.0K
ncbiRefSeq.txt.gz 2021-02-10 15:25 4.5M
ncbiRefSeqCds.sql 2021-02-10 16:00 1.4K
ncbiRefSeqCds.txt.gz 2021-02-10 16:00 565K
ncbiRefSeqCurated.sql 2021-02-10 15:25 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:25 202K
ncbiRefSeqLink.sql 2021-02-10 15:25 2.0K
ncbiRefSeqLink.txt.gz 2021-02-10 15:25 2.5M
ncbiRefSeqOther.sql 2021-02-10 16:00 1.3K
ncbiRefSeqOther.txt.gz 2021-02-10 16:00 75
ncbiRefSeqPepTable.sql 2021-02-10 16:00 1.4K
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:00 13M
ncbiRefSeqPredicted.sql 2021-02-10 15:25 2.0K
ncbiRefSeqPredicted.txt.gz 2021-02-10 15:25 4.4M
ncbiRefSeqPsl.sql 2021-02-10 15:25 2.1K
ncbiRefSeqPsl.txt.gz 2021-02-10 15:25 6.6M
nestedRepeats.sql 2016-10-14 15:45 1.9K
nestedRepeats.txt.gz 2016-10-14 15:45 19M
netGorGor5.sql 2016-10-14 15:45 2.1K
netGorGor5.txt.gz 2016-10-14 15:45 9.5M
netHg38.sql 2016-10-14 15:45 2.1K
netHg38.txt.gz 2016-10-14 15:45 8.1M
netMm10.sql 2016-10-14 15:45 2.1K
netMm10.txt.gz 2016-10-14 15:45 75M
netRn6.sql 2017-03-28 00:55 2.1K
netRn6.txt.gz 2017-03-28 00:57 82M
refFlat.sql 2020-08-22 17:50 1.7K
refFlat.txt.gz 2020-08-22 17:50 206K
refGene.sql 2020-08-22 17:50 1.9K
refGene.txt.gz 2020-08-22 17:50 225K
refSeqAli.sql 2020-08-22 17:50 2.1K
refSeqAli.txt.gz 2020-08-22 17:50 229K
rmsk.sql 2016-10-14 15:38 1.9K
rmsk.txt.gz 2016-10-14 15:39 151M
seqNcbiRefSeq.sql 2021-02-10 16:00 1.6K
seqNcbiRefSeq.txt.gz 2021-02-10 16:00 1.5M
simpleRepeat.sql 2016-10-14 15:41 1.9K
simpleRepeat.txt.gz 2016-10-14 15:41 31M
tableDescriptions.sql 2024-11-23 02:03 1.4K
tableDescriptions.txt.gz 2024-11-23 02:03 6.5K
tableList.sql 2024-11-24 03:06 1.6K
tableList.txt.gz 2024-11-24 03:06 3.7K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 62K
ucscToINSDC.sql 2016-10-14 15:45 1.4K
ucscToINSDC.txt.gz 2016-10-14 15:45 362K
ucscToRefSeq.sql 2016-10-14 15:46 1.4K
ucscToRefSeq.txt.gz 2016-10-14 15:46 353K
windowmaskerSdust.sql 2016-10-14 15:46 1.5K
windowmaskerSdust.txt.gz 2016-10-14 15:46 161M
xenoMrna.sql 2020-08-22 17:50 2.1K
xenoMrna.txt.gz 2020-08-22 17:50 257M
xenoRefFlat.sql 2020-08-22 17:50 1.7K
xenoRefFlat.txt.gz 2020-08-22 17:50 24M
xenoRefGene.sql 2020-08-22 17:50 2.0K
xenoRefGene.txt.gz 2020-08-22 17:50 27M
xenoRefSeqAli.sql 2020-08-22 18:06 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 18:06 25M