This directory contains a dump of the UCSC genome annotation database for the
May. 2012 (Max-Planck/panPan1) assembly of the bonobo genome
(panPan1, Max-Planck Institute panpan1 (GCA_000258665.1)) .
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/382348
http://www.ncbi.nlm.nih.gov/bioproject/49285
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=panPan1
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/panPan1/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/panPan1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/panPan1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan1/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 panPan1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panPan1 --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 -
augustusGene.sql 2015-06-25 14:32 1.9K
augustusGene.txt.gz 2015-06-25 14:32 1.9M
microsat.sql 2015-06-25 14:32 1.5K
microsat.txt.gz 2015-06-25 14:32 288K
chainHg38.sql 2015-06-25 14:32 1.7K
chainHg38.txt.gz 2015-06-25 14:32 113M
chainHg38Link.sql 2015-06-25 14:32 1.5K
chainHg38Link.txt.gz 2015-06-25 14:33 431M
chainTarSyr2.sql 2015-06-25 14:34 1.7K
gc5BaseBw.sql 2015-06-25 14:34 1.3K
gc5BaseBw.txt.gz 2015-06-25 14:34 63
chainTarSyr2.txt.gz 2015-06-25 14:34 123M
chainTarSyr2Link.sql 2015-06-25 14:35 1.5K
chainTarSyr2Link.txt.gz 2015-06-25 14:36 788M
nestedRepeats.sql 2015-06-25 14:39 1.9K
nestedRepeats.txt.gz 2015-06-25 14:39 16M
chromInfo.sql 2015-06-25 14:39 1.4K
chromInfo.txt.gz 2015-06-25 14:39 52K
genscan.sql 2015-06-25 14:39 1.7K
genscan.txt.gz 2015-06-25 14:39 2.4M
cpgIslandExt.sql 2015-06-25 14:39 1.7K
cpgIslandExt.txt.gz 2015-06-25 14:39 564K
cpgIslandExtUnmasked.sql 2015-06-25 14:39 1.7K
cpgIslandExtUnmasked.txt.gz 2015-06-25 14:39 895K
gold.sql 2015-06-25 14:39 1.7K
gold.txt.gz 2015-06-25 14:39 2.0M
cytoBandIdeo.sql 2015-06-25 14:39 1.5K
cytoBandIdeo.txt.gz 2015-06-25 14:39 54K
grp.sql 2015-06-25 14:39 1.3K
grp.txt.gz 2015-06-25 14:39 199
netHg38.sql 2015-06-25 14:39 2.1K
netHg38.txt.gz 2015-06-25 14:39 6.6M
gap.sql 2015-06-25 14:39 1.6K
gap.txt.gz 2015-06-25 14:39 1.8M
history.sql 2015-06-25 14:39 1.6K
history.txt.gz 2015-06-25 14:39 853
netTarSyr2.sql 2015-06-25 14:39 2.1K
netTarSyr2.txt.gz 2015-06-25 14:39 68M
rmsk.sql 2015-06-25 14:39 1.9K
rmsk.txt.gz 2015-06-25 14:39 128M
simpleRepeat.sql 2015-06-25 14:40 1.9K
simpleRepeat.txt.gz 2015-06-25 14:40 21M
ucscToINSDC.sql 2015-06-25 14:40 1.4K
ucscToINSDC.txt.gz 2015-06-25 14:40 80K
windowmaskerSdust.sql 2015-06-25 14:40 1.5K
windowmaskerSdust.txt.gz 2015-06-25 14:40 142M
geneid.sql 2015-11-22 20:17 1.9K
geneid.txt.gz 2015-11-22 20:17 1.7M
ncbiRefSeq.sql 2018-02-09 13:47 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:47 2.9M
ncbiRefSeqCurated.sql 2018-02-09 13:47 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:47 4.3K
ncbiRefSeqPredicted.sql 2018-02-09 13:47 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:47 2.9M
ncbiRefSeqLink.sql 2018-02-09 13:47 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:47 1.4M
ncbiRefSeqPsl.sql 2018-02-09 13:47 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:47 3.8M
chromAlias.sql 2018-02-18 08:01 1.4K
chromAlias.txt.gz 2018-02-18 08:01 106K
ucscToRefSeq.sql 2018-02-18 08:01 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:01 80K
all_mrna.sql 2018-04-08 07:49 2.1K
all_mrna.txt.gz 2018-04-08 07:49 8.5K
extNcbiRefSeq.sql 2018-08-14 02:21 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:21 91
ncbiRefSeqCds.sql 2018-08-14 02:21 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:21 310K
ncbiRefSeqOther.sql 2018-08-14 02:21 1.3K
ncbiRefSeqOther.txt.gz 2018-08-14 02:21 75
ncbiRefSeqPepTable.sql 2018-08-14 02:21 1.4K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:21 8.8M
seqNcbiRefSeq.sql 2018-08-14 02:21 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:21 780K
mrnaOrientInfo.sql 2019-07-28 06:00 1.8K
mrnaOrientInfo.txt.gz 2019-07-28 06:00 3.8K
refSeqAli.sql 2019-07-28 06:00 2.1K
refSeqAli.txt.gz 2019-07-28 06:00 5.9K
refGene.sql 2020-08-22 17:50 1.9K
refGene.txt.gz 2020-08-22 17:50 5.6K
refFlat.sql 2020-08-22 17:50 1.7K
refFlat.txt.gz 2020-08-22 17:50 5.0K
xenoRefGene.sql 2020-08-22 17:50 2.0K
xenoRefGene.txt.gz 2020-08-22 17:50 39M
xenoRefFlat.sql 2020-08-22 17:50 1.7K
xenoRefFlat.txt.gz 2020-08-22 17:50 35M
xenoRefSeqAli.sql 2020-08-22 17:50 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 17:50 37M
gbLoaded.sql 2020-08-22 17:50 1.6K
gbLoaded.txt.gz 2020-08-22 17:50 18K
trackDb.sql 2023-12-05 13:50 2.1K
trackDb.txt.gz 2023-12-05 13:50 29K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:50 29K
hgFindSpec.sql 2023-12-05 13:50 1.8K
hgFindSpec.txt.gz 2023-12-05 13:50 1.1K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.1K
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 6.1K
tableList.sql 2024-04-14 03:17 1.6K
tableList.txt.gz 2024-04-14 03:17 3.1K
bigFiles.sql 2024-04-14 03:17 1.4K
bigFiles.txt.gz 2024-04-14 03:17 94