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.
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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 -
chainRn6Link.txt.gz 2017-03-27 23:19 3.0G
chainRn6.txt.gz 2017-03-27 22:13 1.0G
chainMm10Link.txt.gz 2016-10-14 15:42 542M
xenoMrna.txt.gz 2020-08-22 17:50 257M
chainGorGor5Link.txt.gz 2016-10-14 15:37 253M
chainHg38Link.txt.gz 2016-10-14 15:40 222M
windowmaskerSdust.txt.gz 2016-10-14 15:46 161M
rmsk.txt.gz 2016-10-14 15:39 151M
chainGorGor5.txt.gz 2016-10-14 15:37 83M
netRn6.txt.gz 2017-03-28 00:57 82M
netMm10.txt.gz 2016-10-14 15:45 75M
chainMm10.txt.gz 2016-10-14 15:41 67M
chainHg38.txt.gz 2016-10-14 15:39 61M
simpleRepeat.txt.gz 2016-10-14 15:41 31M
xenoRefGene.txt.gz 2020-08-22 17:50 27M
xenoRefSeqAli.txt.gz 2020-08-22 18:06 25M
xenoRefFlat.txt.gz 2020-08-22 17:50 24M
nestedRepeats.txt.gz 2016-10-14 15:45 19M
ensPep.txt.gz 2021-05-25 14:44 15M
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:00 13M
netGorGor5.txt.gz 2016-10-14 15:45 9.5M
netHg38.txt.gz 2016-10-14 15:45 8.1M
ncbiRefSeqPsl.txt.gz 2021-02-10 15:25 6.6M
ncbiRefSeq.txt.gz 2021-02-10 15:25 4.5M
ncbiRefSeqPredicted.txt.gz 2021-02-10 15:25 4.4M
ensGene.txt.gz 2021-05-25 14:43 3.5M
genscan.txt.gz 2016-10-14 15:45 3.1M
ncbiRefSeqLink.txt.gz 2021-02-10 15:25 2.5M
augustusGene.txt.gz 2016-10-14 15:36 2.4M
seqNcbiRefSeq.txt.gz 2021-02-10 16:00 1.5M
gbMiscDiff.txt.gz 2016-10-14 15:45 1.2M
cpgIslandExtUnmasked.txt.gz 2016-10-14 15:45 1.1M
gold.txt.gz 2016-10-14 15:46 1.1M
all_est.txt.gz 2016-10-14 15:36 889K
cpgIslandExt.txt.gz 2016-10-14 15:45 707K
intronEst.txt.gz 2016-10-14 15:37 705K
ensGtp.txt.gz 2021-05-25 14:43 617K
ncbiRefSeqCds.txt.gz 2021-02-10 16:00 565K
chromAlias.txt.gz 2018-02-04 08:54 467K
gap.txt.gz 2016-10-14 15:45 364K
ucscToINSDC.txt.gz 2016-10-14 15:45 362K
ucscToRefSeq.txt.gz 2016-10-14 15:46 353K
microsat.txt.gz 2016-10-14 15:40 347K
ensemblToGeneName.txt.gz 2021-05-25 14:43 310K
all_mrna.txt.gz 2020-08-22 17:50 309K
cytoBandIdeo.txt.gz 2016-10-14 15:45 235K
estOrientInfo.txt.gz 2016-10-14 15:45 231K
refSeqAli.txt.gz 2020-08-22 17:50 229K
refGene.txt.gz 2020-08-22 17:50 225K
chromInfo.txt.gz 2016-10-14 15:45 218K
refFlat.txt.gz 2020-08-22 17:50 206K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:25 202K
ensemblSource.txt.gz 2021-05-25 14:44 181K
mrnaOrientInfo.txt.gz 2020-08-22 17:50 115K
trackDb.txt.gz 2024-07-25 09:34 62K
gbLoaded.txt.gz 2020-08-22 18:06 38K
tableDescriptions.txt.gz 2024-11-23 02:03 6.5K
tableList.txt.gz 2024-11-24 03:06 3.7K
xenoRefSeqAli.sql 2020-08-22 18:06 2.1K
ncbiRefSeqPsl.sql 2021-02-10 15:25 2.1K
refSeqAli.sql 2020-08-22 17:50 2.1K
xenoMrna.sql 2020-08-22 17:50 2.1K
all_mrna.sql 2020-08-22 17:50 2.1K
intronEst.sql 2016-10-14 15:37 2.1K
all_est.sql 2016-10-14 15:36 2.1K
netGorGor5.sql 2016-10-14 15:45 2.1K
netMm10.sql 2016-10-14 15:45 2.1K
netHg38.sql 2016-10-14 15:45 2.1K
netRn6.sql 2017-03-28 00:55 2.1K
trackDb.sql 2024-07-25 09:34 2.1K
ncbiRefSeqLink.sql 2021-02-10 15:25 2.0K
ncbiRefSeqPredicted.sql 2021-02-10 15:25 2.0K
ncbiRefSeqCurated.sql 2021-02-10 15:25 2.0K
xenoRefGene.sql 2020-08-22 17:50 2.0K
ncbiRefSeq.sql 2021-02-10 15:25 2.0K
refGene.sql 2020-08-22 17:50 1.9K
ensGene.sql 2021-05-25 14:43 1.9K
augustusGene.sql 2016-10-14 15:36 1.9K
nestedRepeats.sql 2016-10-14 15:45 1.9K
simpleRepeat.sql 2016-10-14 15:41 1.9K
rmsk.sql 2016-10-14 15:38 1.9K
mrnaOrientInfo.sql 2020-08-22 17:50 1.8K
estOrientInfo.sql 2016-10-14 15:45 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
xenoRefFlat.sql 2020-08-22 17:50 1.7K
refFlat.sql 2020-08-22 17:50 1.7K
cpgIslandExtUnmasked.sql 2016-10-14 15:45 1.7K
chainGorGor5.sql 2016-10-14 15:36 1.7K
chainMm10.sql 2016-10-14 15:41 1.7K
chainHg38.sql 2016-10-14 15:39 1.7K
chainRn6.sql 2017-03-27 22:02 1.7K
cpgIslandExt.sql 2016-10-14 15:45 1.7K
genscan.sql 2016-10-14 15:45 1.7K
gold.sql 2016-10-14 15:46 1.7K
gbLoaded.sql 2020-08-22 18:06 1.6K
gap.sql 2016-10-14 15:45 1.6K
history.sql 2016-10-14 15:36 1.6K
seqNcbiRefSeq.sql 2021-02-10 16:00 1.6K
tableList.sql 2024-11-24 03:06 1.6K
chainGorGor5Link.sql 2016-10-14 15:37 1.5K
chainMm10Link.sql 2016-10-14 15:41 1.5K
chainHg38Link.sql 2016-10-14 15:40 1.5K
chainRn6Link.sql 2017-03-27 22:47 1.5K
cytoBandIdeo.sql 2016-10-14 15:45 1.5K
windowmaskerSdust.sql 2016-10-14 15:46 1.5K
microsat.sql 2016-10-14 15:40 1.5K
extNcbiRefSeq.sql 2021-02-10 16:00 1.5K
gbMiscDiff.sql 2016-10-14 15:45 1.5K
ensGtp.sql 2021-05-25 14:43 1.4K
ucscToRefSeq.sql 2016-10-14 15:46 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
ucscToINSDC.sql 2016-10-14 15:45 1.4K
chromAlias.sql 2018-02-04 08:54 1.4K
ensemblToGeneName.sql 2021-05-25 14:43 1.4K
chromInfo.sql 2016-10-14 15:45 1.4K
ncbiRefSeqPepTable.sql 2021-02-10 16:00 1.4K
bigFiles.sql 2024-11-24 03:06 1.4K
ensemblSource.sql 2021-05-25 14:44 1.4K
ncbiRefSeqCds.sql 2021-02-10 16:00 1.4K
grp.sql 2016-10-14 15:46 1.3K
ensPep.sql 2021-05-25 14:44 1.3K
ncbiRefSeqOther.sql 2021-02-10 16:00 1.3K
gc5BaseBw.sql 2016-10-14 15:46 1.3K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
history.txt.gz 2016-10-14 15:36 614
grp.txt.gz 2016-10-14 15:46 213
bigFiles.txt.gz 2024-11-24 03:06 95
extNcbiRefSeq.txt.gz 2021-02-10 16:00 91
ncbiRefSeqOther.txt.gz 2021-02-10 16:00 75
gc5BaseBw.txt.gz 2016-10-14 15:46 66