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.
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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 -
chainTarSyr2Link.txt.gz 2015-06-25 14:36 788M
chainHg38Link.txt.gz 2015-06-25 14:33 431M
windowmaskerSdust.txt.gz 2015-06-25 14:40 142M
rmsk.txt.gz 2015-06-25 14:39 128M
chainTarSyr2.txt.gz 2015-06-25 14:34 123M
chainHg38.txt.gz 2015-06-25 14:32 113M
netTarSyr2.txt.gz 2015-06-25 14:39 68M
xenoRefGene.txt.gz 2020-08-22 17:50 39M
xenoRefSeqAli.txt.gz 2020-08-22 17:50 37M
xenoRefFlat.txt.gz 2020-08-22 17:50 35M
simpleRepeat.txt.gz 2015-06-25 14:40 21M
nestedRepeats.txt.gz 2015-06-25 14:39 16M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:21 8.8M
netHg38.txt.gz 2015-06-25 14:39 6.6M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:47 3.8M
ncbiRefSeq.txt.gz 2018-02-09 13:47 2.9M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:47 2.9M
genscan.txt.gz 2015-06-25 14:39 2.4M
gold.txt.gz 2015-06-25 14:39 2.0M
augustusGene.txt.gz 2015-06-25 14:32 1.9M
gap.txt.gz 2015-06-25 14:39 1.8M
geneid.txt.gz 2015-11-22 20:17 1.7M
ncbiRefSeqLink.txt.gz 2018-02-09 13:47 1.4M
cpgIslandExtUnmasked.txt.gz 2015-06-25 14:39 895K
seqNcbiRefSeq.txt.gz 2018-08-14 02:21 780K
cpgIslandExt.txt.gz 2015-06-25 14:39 564K
ncbiRefSeqCds.txt.gz 2018-08-14 02:21 310K
microsat.txt.gz 2015-06-25 14:32 288K
chromAlias.txt.gz 2018-02-18 08:01 106K
ucscToINSDC.txt.gz 2015-06-25 14:40 80K
ucscToRefSeq.txt.gz 2018-02-18 08:01 80K
cytoBandIdeo.txt.gz 2015-06-25 14:39 54K
chromInfo.txt.gz 2015-06-25 14:39 52K
trackDb.txt.gz 2023-12-05 13:50 29K
gbLoaded.txt.gz 2020-08-22 17:50 18K
all_mrna.txt.gz 2018-04-08 07:49 8.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.1K
refSeqAli.txt.gz 2019-07-28 06:00 5.9K
refGene.txt.gz 2020-08-22 17:50 5.6K
refFlat.txt.gz 2020-08-22 17:50 5.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:47 4.3K
mrnaOrientInfo.txt.gz 2019-07-28 06:00 3.8K
tableList.txt.gz 2024-12-08 03:16 3.0K
xenoRefSeqAli.sql 2020-08-22 17:50 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:47 2.1K
refSeqAli.sql 2019-07-28 06:00 2.1K
all_mrna.sql 2018-04-08 07:49 2.1K
netTarSyr2.sql 2015-06-25 14:39 2.1K
netHg38.sql 2015-06-25 14:39 2.1K
trackDb.sql 2023-12-05 13:50 2.1K
ncbiRefSeqLink.sql 2018-02-09 13:47 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:47 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:47 2.0K
xenoRefGene.sql 2020-08-22 17:50 2.0K
ncbiRefSeq.sql 2018-02-09 13:47 2.0K
refGene.sql 2020-08-22 17:50 1.9K
augustusGene.sql 2015-06-25 14:32 1.9K
nestedRepeats.sql 2015-06-25 14:39 1.9K
simpleRepeat.sql 2015-06-25 14:40 1.9K
geneid.sql 2015-11-22 20:17 1.9K
rmsk.sql 2015-06-25 14:39 1.9K
mrnaOrientInfo.sql 2019-07-28 06:00 1.8K
hgFindSpec.sql 2023-12-05 13:50 1.8K
xenoRefFlat.sql 2020-08-22 17:50 1.7K
refFlat.sql 2020-08-22 17:50 1.7K
cpgIslandExtUnmasked.sql 2015-06-25 14:39 1.7K
chainTarSyr2.sql 2015-06-25 14:34 1.7K
chainHg38.sql 2015-06-25 14:32 1.7K
cpgIslandExt.sql 2015-06-25 14:39 1.7K
genscan.sql 2015-06-25 14:39 1.7K
gold.sql 2015-06-25 14:39 1.7K
gbLoaded.sql 2020-08-22 17:50 1.6K
gap.sql 2015-06-25 14:39 1.6K
tableList.sql 2024-12-08 03:16 1.6K
history.sql 2015-06-25 14:39 1.6K
seqNcbiRefSeq.sql 2018-08-14 02:21 1.6K
chainTarSyr2Link.sql 2015-06-25 14:35 1.5K
chainHg38Link.sql 2015-06-25 14:32 1.5K
cytoBandIdeo.sql 2015-06-25 14:39 1.5K
windowmaskerSdust.sql 2015-06-25 14:40 1.5K
microsat.sql 2015-06-25 14:32 1.5K
extNcbiRefSeq.sql 2018-08-14 02:21 1.5K
tableDescriptions.sql 2024-12-07 02:03 1.5K
ucscToRefSeq.sql 2018-02-18 08:01 1.4K
ucscToINSDC.sql 2015-06-25 14:40 1.4K
chromAlias.sql 2018-02-18 08:01 1.4K
bigFiles.sql 2024-12-08 03:16 1.4K
chromInfo.sql 2015-06-25 14:39 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:21 1.4K
ncbiRefSeqCds.sql 2018-08-14 02:21 1.4K
grp.sql 2015-06-25 14:39 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:21 1.3K
gc5BaseBw.sql 2015-06-25 14:34 1.3K
hgFindSpec.txt.gz 2023-12-05 13:50 1.1K
history.txt.gz 2015-06-25 14:39 853
grp.txt.gz 2015-06-25 14:39 199
bigFiles.txt.gz 2024-12-08 03:16 94
extNcbiRefSeq.txt.gz 2018-08-14 02:21 91
ncbiRefSeqOther.txt.gz 2018-08-14 02:21 75
gc5BaseBw.txt.gz 2015-06-25 14:34 63