This directory contains a dump of the UCSC genome annotation database for the
May 2020 (Mhudiblu_PPA_v0/panPan3) assembly of the bonobo genome
(panPan3, University of Washington) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/10729
https://www.ncbi.nlm.nih.gov/genome/assembly/7133581
https://www.ncbi.nlm.nih.gov/bioproject/526933
https://www.ncbi.nlm.nih.gov/biosample/SAMN11123633
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=panPan3
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.soe.ucsc.edu, then go to
the directory goldenPath/panPan3/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.soe.ucsc.edu/goldenPath/panPan3/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/panPan3/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan3/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 panPan3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panPan3 --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 -
gold.sql 2020-06-12 10:45 1.7K
gold.txt.gz 2020-06-12 10:45 66K
gap.sql 2020-06-12 10:45 1.6K
gap.txt.gz 2020-06-12 10:45 11K
cpgIslandExtUnmasked.sql 2020-06-12 11:36 1.7K
cpgIslandExtUnmasked.txt.gz 2020-06-12 11:36 1.0M
chromAlias.sql 2020-06-12 12:33 1.4K
chromAlias.txt.gz 2020-06-12 12:33 93K
simpleRepeat.sql 2020-06-12 17:08 1.9K
simpleRepeat.txt.gz 2020-06-12 17:08 26M
cytoBandIdeo.sql 2020-06-12 17:27 1.5K
cytoBandIdeo.txt.gz 2020-06-12 17:27 27K
gc5BaseBw.sql 2020-06-12 17:27 1.3K
gc5BaseBw.txt.gz 2020-06-12 17:27 66
grp.sql 2020-06-12 17:27 1.4K
grp.txt.gz 2020-06-12 17:27 213
ucscToRefSeq.sql 2020-06-12 17:27 1.5K
ucscToRefSeq.txt.gz 2020-06-12 17:27 37K
ucscToINSDC.sql 2020-06-12 17:27 1.4K
ucscToINSDC.txt.gz 2020-06-12 17:27 39K
chromInfo.sql 2020-06-12 18:00 1.4K
chromInfo.txt.gz 2020-06-12 18:00 27K
rmsk.sql 2020-06-12 18:21 1.9K
rmsk.txt.gz 2020-06-12 18:21 139M
nestedRepeats.sql 2020-06-12 18:23 2.0K
nestedRepeats.txt.gz 2020-06-12 18:23 18M
windowmaskerSdust.sql 2020-06-12 19:56 1.5K
windowmaskerSdust.txt.gz 2020-06-12 19:56 145M
microsat.sql 2020-06-13 10:04 1.5K
microsat.txt.gz 2020-06-13 10:04 304K
ncbiRefSeq.sql 2020-06-13 10:16 2.0K
ncbiRefSeq.txt.gz 2020-06-13 10:16 4.0M
ncbiRefSeqCurated.sql 2020-06-13 10:16 2.0K
ncbiRefSeqCurated.txt.gz 2020-06-13 10:16 8.5K
ncbiRefSeqPredicted.sql 2020-06-13 10:16 2.0K
ncbiRefSeqPredicted.txt.gz 2020-06-13 10:16 4.0M
ncbiRefSeqLink.sql 2020-06-13 10:16 2.0K
ncbiRefSeqLink.txt.gz 2020-06-13 10:16 2.2M
ncbiRefSeqPsl.sql 2020-06-13 10:16 2.1K
ncbiRefSeqPsl.txt.gz 2020-06-13 10:16 5.7M
ncbiRefSeqOther.sql 2020-06-13 15:32 1.3K
ncbiRefSeqOther.txt.gz 2020-06-13 15:32 75
ncbiRefSeqPepTable.sql 2020-06-13 15:32 1.4K
ncbiRefSeqPepTable.txt.gz 2020-06-13 15:32 12M
extNcbiRefSeq.sql 2020-06-13 15:42 1.5K
extNcbiRefSeq.txt.gz 2020-06-13 15:42 91
seqNcbiRefSeq.sql 2020-06-13 15:42 1.6K
seqNcbiRefSeq.txt.gz 2020-06-13 15:42 1.3M
ncbiRefSeqCds.sql 2020-06-13 15:42 1.4K
ncbiRefSeqCds.txt.gz 2020-06-13 15:42 500K
cpgIslandExt.sql 2020-06-15 09:12 1.7K
cpgIslandExt.txt.gz 2020-06-15 09:12 625K
augustusGene.sql 2020-06-15 12:26 2.0K
augustusGene.txt.gz 2020-06-15 12:26 2.3M
chainHg38.sql 2020-06-15 13:06 1.7K
chainHg38.txt.gz 2020-06-15 13:06 56M
chainHg38Link.sql 2020-06-15 13:07 1.6K
chainHg38Link.txt.gz 2020-06-15 13:07 164M
netHg38.sql 2020-06-15 13:09 2.1K
netHg38.txt.gz 2020-06-15 13:09 5.9M
genscan.sql 2020-06-15 13:18 1.7K
genscan.txt.gz 2020-06-15 13:18 2.8M
chainMm10.sql 2020-06-15 17:21 1.7K
chainMm10.txt.gz 2020-06-15 17:21 67M
chainMm10Link.sql 2020-06-15 17:25 1.6K
chainMm10Link.txt.gz 2020-06-15 17:25 524M
netMm10.sql 2020-06-15 17:28 2.1K
netMm10.txt.gz 2020-06-15 17:28 75M
all_mrna.sql 2020-06-16 17:21 2.1K
all_mrna.txt.gz 2020-06-16 17:21 14K
refGene.sql 2020-06-16 17:28 1.9K
refGene.txt.gz 2020-06-16 17:28 8.0K
refFlat.sql 2020-06-16 17:28 1.7K
refFlat.txt.gz 2020-06-16 17:28 7.1K
xenoRefGene.sql 2020-06-16 17:28 2.0K
xenoRefGene.txt.gz 2020-06-16 17:28 12M
xenoRefFlat.sql 2020-06-16 17:28 1.7K
xenoRefFlat.txt.gz 2020-06-16 17:28 10M
refSeqAli.sql 2020-06-16 17:28 2.1K
refSeqAli.txt.gz 2020-06-16 17:28 8.3K
xenoRefSeqAli.sql 2020-06-16 17:28 2.1K
xenoRefSeqAli.txt.gz 2020-06-16 17:28 20M
mrnaOrientInfo.sql 2020-06-16 17:31 1.8K
mrnaOrientInfo.txt.gz 2020-06-16 17:31 8.7K
gbLoaded.sql 2020-06-16 17:31 1.6K
gbLoaded.txt.gz 2020-06-16 17:31 392
crisprAllRanges.sql 2020-06-21 18:45 1.5K
crisprAllRanges.txt.gz 2020-06-21 18:45 9.6K
crisprAllTargets.sql 2020-06-22 01:13 1.3K
crisprAllTargets.txt.gz 2020-06-22 01:13 69
history.sql 2020-06-22 01:39 1.6K
history.txt.gz 2020-06-22 01:39 896
chainMm39.sql 2020-11-24 11:33 1.7K
chainMm39.txt.gz 2020-11-24 11:33 92M
chainMm39Link.sql 2020-11-24 11:37 1.6K
chainMm39Link.txt.gz 2020-11-24 11:37 557M
netMm39.sql 2020-11-24 11:41 2.1K
netMm39.txt.gz 2020-11-24 11:41 83M
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 42K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
tableDescriptions.sql 2024-11-16 02:04 1.5K
tableDescriptions.txt.gz 2024-11-16 02:04 6.2K
tableList.sql 2024-11-17 03:13 1.6K
tableList.txt.gz 2024-11-17 03:13 3.0K
bigFiles.sql 2024-11-17 03:13 1.4K
bigFiles.txt.gz 2024-11-17 03:13 119