This directory contains a dump of the UCSC genome annotation database for the
Aug. 2015 (MPI-EVA panpan1.1/panPan2) assembly of the bonobo genome
(panPan2, Max-Planck Institute for Evolutionary Anthropology) .
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/10729
http://www.ncbi.nlm.nih.gov/genome/assembly/474211
http://www.ncbi.nlm.nih.gov/bioproject/169343
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=panPan2
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/panPan2/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/panPan2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/panPan2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan2/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 panPan2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panPan2 --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_mrna.sql 2020-08-22 17:09 2.1K
all_mrna.txt.gz 2020-08-22 17:09 14K
augustusGene.sql 2017-12-20 11:12 1.9K
augustusGene.txt.gz 2017-12-20 11:12 2.2M
bigFiles.sql 2024-04-14 03:06 1.4K
bigFiles.txt.gz 2024-04-14 03:06 95
chainGorGor5.sql 2017-12-20 11:12 1.7K
chainGorGor5.txt.gz 2017-12-20 11:12 11M
chainGorGor5Link.sql 2017-12-20 11:12 1.5K
chainGorGor5Link.txt.gz 2017-12-20 11:12 110M
chainHg38.sql 2017-12-20 11:13 1.7K
chainHg38.txt.gz 2017-12-20 11:13 37M
chainHg38Link.sql 2017-12-20 11:13 1.5K
chainHg38Link.txt.gz 2017-12-20 11:13 130M
chainMm10.sql 2017-12-20 11:14 1.7K
chainMm10.txt.gz 2017-12-20 11:14 56M
chainMm10Link.sql 2017-12-20 11:14 1.5K
chainMm10Link.txt.gz 2017-12-20 11:15 484M
chainPanTro4.sql 2017-12-20 11:17 1.7K
chainPanTro4.txt.gz 2017-12-20 11:17 19M
chainPanTro4Link.sql 2017-12-20 11:17 1.5K
chainPanTro4Link.txt.gz 2017-12-20 11:17 77M
chromAlias.sql 2017-12-20 11:17 1.4K
chromAlias.txt.gz 2017-12-20 11:17 105K
chromInfo.sql 2017-12-20 11:17 1.4K
chromInfo.txt.gz 2017-12-20 11:17 48K
cpgIslandExt.sql 2017-12-20 11:17 1.7K
cpgIslandExt.txt.gz 2017-12-20 11:17 589K
cpgIslandExtUnmasked.sql 2017-12-20 11:17 1.7K
cpgIslandExtUnmasked.txt.gz 2017-12-20 11:17 920K
cytoBandIdeo.sql 2017-12-20 11:18 1.5K
cytoBandIdeo.txt.gz 2017-12-20 11:18 54K
ensGene.sql 2021-05-25 14:42 1.9K
ensGene.txt.gz 2021-05-25 14:42 3.1M
ensGtp.sql 2021-05-25 14:42 1.4K
ensGtp.txt.gz 2021-05-25 14:42 437K
ensPep.sql 2021-05-25 14:43 1.3K
ensPep.txt.gz 2021-05-25 14:43 7.0M
ensemblSource.sql 2021-05-25 14:43 1.4K
ensemblSource.txt.gz 2021-05-25 14:43 149K
ensemblToGeneName.sql 2021-05-25 14:42 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:42 199K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
gap.sql 2017-12-20 11:18 1.6K
gap.txt.gz 2017-12-20 11:18 1.4M
gapOverlap.sql 2017-12-20 11:18 1.8K
gapOverlap.txt.gz 2017-12-20 11:18 2.3K
gbLoaded.sql 2020-08-22 17:50 1.6K
gbLoaded.txt.gz 2020-08-22 17:50 13K
gc5BaseBw.sql 2017-12-20 11:12 1.3K
gc5BaseBw.txt.gz 2017-12-20 11:12 66
genscan.sql 2017-12-20 11:12 1.7K
genscan.txt.gz 2017-12-20 11:12 2.5M
genscanSubopt.sql 2017-12-20 11:13 1.6K
genscanSubopt.txt.gz 2017-12-20 11:13 5.1M
gold.sql 2017-12-20 11:14 1.7K
gold.txt.gz 2017-12-20 11:14 2.1M
grp.sql 2017-12-20 11:17 1.3K
grp.txt.gz 2017-12-20 11:17 213
hgFindSpec.sql 2023-12-05 13:50 1.8K
hgFindSpec.txt.gz 2023-12-05 13:50 1.2K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.2K
history.sql 2017-12-20 11:17 1.6K
history.txt.gz 2017-12-20 11:17 1.0K
microsat.sql 2017-12-20 11:17 1.5K
microsat.txt.gz 2017-12-20 11:17 298K
mrnaOrientInfo.sql 2020-08-22 17:09 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 17:09 8.5K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 3.2M
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 351K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 6.1K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 10M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.2M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M
nestedRepeats.sql 2017-12-20 11:18 1.9K
nestedRepeats.txt.gz 2017-12-20 11:18 17M
netGorGor5.sql 2017-12-20 11:12 2.1K
netGorGor5.txt.gz 2017-12-20 11:12 7.0M
netHg38.sql 2017-12-20 11:13 2.1K
netHg38.txt.gz 2017-12-20 11:13 6.2M
netMm10.sql 2017-12-20 11:14 2.1K
netMm10.txt.gz 2017-12-20 11:14 71M
netPanTro4.sql 2017-12-20 11:17 2.1K
netPanTro4.txt.gz 2017-12-20 11:17 6.4M
refFlat.sql 2020-08-22 17:28 1.7K
refFlat.txt.gz 2020-08-22 17:28 7.1K
refGene.sql 2020-08-22 17:25 1.9K
refGene.txt.gz 2020-08-22 17:25 8.1K
refSeqAli.sql 2019-07-28 06:01 2.1K
refSeqAli.txt.gz 2019-07-28 06:01 8.2K
rmsk.sql 2017-12-20 11:18 1.9K
rmsk.txt.gz 2017-12-20 11:18 134M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 903K
simpleRepeat.sql 2017-12-20 11:18 1.9K
simpleRepeat.txt.gz 2017-12-20 11:18 21M
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 6.7K
tableList.sql 2024-04-14 03:06 1.6K
tableList.txt.gz 2024-04-14 03:06 3.7K
tandemDups.sql 2017-12-20 11:18 1.8K
tandemDups.txt.gz 2017-12-20 11:18 16M
trackDb.sql 2023-12-05 13:50 2.1K
trackDb.txt.gz 2023-12-05 13:50 32K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:50 32K
ucscToINSDC.sql 2017-12-20 11:18 1.4K
ucscToINSDC.txt.gz 2017-12-20 11:18 79K
ucscToRefSeq.sql 2017-12-20 11:18 1.4K
ucscToRefSeq.txt.gz 2017-12-20 11:18 79K
windowmaskerSdust.sql 2017-12-20 11:18 1.5K
windowmaskerSdust.txt.gz 2017-12-20 11:19 142M
xenoRefFlat.sql 2020-08-22 17:50 1.7K
xenoRefFlat.txt.gz 2020-08-22 17:50 23M
xenoRefGene.sql 2020-08-22 17:50 2.0K
xenoRefGene.txt.gz 2020-08-22 17:50 26M
xenoRefSeqAli.sql 2020-08-22 17:50 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 17:50 24M