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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
gc5BaseBw.txt.gz 2020-06-12 17:27 66
crisprAllTargets.txt.gz 2020-06-22 01:13 69
ncbiRefSeqOther.txt.gz 2020-06-13 15:32 75
extNcbiRefSeq.txt.gz 2020-06-13 15:42 91
bigFiles.txt.gz 2024-12-29 03:03 119
grp.txt.gz 2020-06-12 17:27 213
gbLoaded.txt.gz 2020-06-16 17:31 392
history.txt.gz 2020-06-22 01:39 896
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
gc5BaseBw.sql 2020-06-12 17:27 1.3K
ncbiRefSeqOther.sql 2020-06-13 15:32 1.3K
crisprAllTargets.sql 2020-06-22 01:13 1.3K
ncbiRefSeqCds.sql 2020-06-13 15:42 1.4K
grp.sql 2020-06-12 17:27 1.4K
ncbiRefSeqPepTable.sql 2020-06-13 15:32 1.4K
bigFiles.sql 2024-12-29 03:03 1.4K
chromInfo.sql 2020-06-12 18:00 1.4K
chromAlias.sql 2020-06-12 12:33 1.4K
ucscToINSDC.sql 2020-06-12 17:27 1.4K
ucscToRefSeq.sql 2020-06-12 17:27 1.5K
tableDescriptions.sql 2024-12-28 02:12 1.5K
extNcbiRefSeq.sql 2020-06-13 15:42 1.5K
microsat.sql 2020-06-13 10:04 1.5K
crisprAllRanges.sql 2020-06-21 18:45 1.5K
windowmaskerSdust.sql 2020-06-12 19:56 1.5K
cytoBandIdeo.sql 2020-06-12 17:27 1.5K
chainHg38Link.sql 2020-06-15 13:07 1.6K
chainMm10Link.sql 2020-06-15 17:25 1.6K
chainMm39Link.sql 2020-11-24 11:37 1.6K
seqNcbiRefSeq.sql 2020-06-13 15:42 1.6K
tableList.sql 2024-12-29 03:03 1.6K
history.sql 2020-06-22 01:39 1.6K
gbLoaded.sql 2020-06-16 17:31 1.6K
gap.sql 2020-06-12 10:45 1.6K
gold.sql 2020-06-12 10:45 1.7K
genscan.sql 2020-06-15 13:18 1.7K
cpgIslandExt.sql 2020-06-15 09:12 1.7K
chainHg38.sql 2020-06-15 13:06 1.7K
chainMm10.sql 2020-06-15 17:21 1.7K
chainMm39.sql 2020-11-24 11:33 1.7K
refFlat.sql 2020-06-16 17:28 1.7K
cpgIslandExtUnmasked.sql 2020-06-12 11:36 1.7K
xenoRefFlat.sql 2020-06-16 17:28 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
mrnaOrientInfo.sql 2020-06-16 17:31 1.8K
rmsk.sql 2020-06-12 18:21 1.9K
refGene.sql 2020-06-16 17:28 1.9K
simpleRepeat.sql 2020-06-12 17:08 1.9K
ncbiRefSeq.sql 2020-06-13 10:16 2.0K
nestedRepeats.sql 2020-06-12 18:23 2.0K
xenoRefGene.sql 2020-06-16 17:28 2.0K
augustusGene.sql 2020-06-15 12:26 2.0K
ncbiRefSeqCurated.sql 2020-06-13 10:16 2.0K
ncbiRefSeqPredicted.sql 2020-06-13 10:16 2.0K
ncbiRefSeqLink.sql 2020-06-13 10:16 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netHg38.sql 2020-06-15 13:09 2.1K
netMm10.sql 2020-06-15 17:28 2.1K
netMm39.sql 2020-11-24 11:41 2.1K
all_mrna.sql 2020-06-16 17:21 2.1K
refSeqAli.sql 2020-06-16 17:28 2.1K
ncbiRefSeqPsl.sql 2020-06-13 10:16 2.1K
xenoRefSeqAli.sql 2020-06-16 17:28 2.1K
tableList.txt.gz 2024-12-29 03:03 3.0K
tableDescriptions.txt.gz 2024-12-28 02:12 6.2K
refFlat.txt.gz 2020-06-16 17:28 7.1K
refGene.txt.gz 2020-06-16 17:28 8.0K
refSeqAli.txt.gz 2020-06-16 17:28 8.3K
ncbiRefSeqCurated.txt.gz 2020-06-13 10:16 8.5K
mrnaOrientInfo.txt.gz 2020-06-16 17:31 8.7K
crisprAllRanges.txt.gz 2020-06-21 18:45 9.6K
gap.txt.gz 2020-06-12 10:45 11K
all_mrna.txt.gz 2020-06-16 17:21 14K
chromInfo.txt.gz 2020-06-12 18:00 27K
cytoBandIdeo.txt.gz 2020-06-12 17:27 27K
ucscToRefSeq.txt.gz 2020-06-12 17:27 37K
ucscToINSDC.txt.gz 2020-06-12 17:27 39K
trackDb.txt.gz 2024-01-31 15:13 42K
gold.txt.gz 2020-06-12 10:45 66K
chromAlias.txt.gz 2020-06-12 12:33 93K
microsat.txt.gz 2020-06-13 10:04 304K
ncbiRefSeqCds.txt.gz 2020-06-13 15:42 500K
cpgIslandExt.txt.gz 2020-06-15 09:12 625K
cpgIslandExtUnmasked.txt.gz 2020-06-12 11:36 1.0M
seqNcbiRefSeq.txt.gz 2020-06-13 15:42 1.3M
ncbiRefSeqLink.txt.gz 2020-06-13 10:16 2.2M
augustusGene.txt.gz 2020-06-15 12:26 2.3M
genscan.txt.gz 2020-06-15 13:18 2.8M
ncbiRefSeqPredicted.txt.gz 2020-06-13 10:16 4.0M
ncbiRefSeq.txt.gz 2020-06-13 10:16 4.0M
ncbiRefSeqPsl.txt.gz 2020-06-13 10:16 5.7M
netHg38.txt.gz 2020-06-15 13:09 5.9M
xenoRefFlat.txt.gz 2020-06-16 17:28 10M
xenoRefGene.txt.gz 2020-06-16 17:28 12M
ncbiRefSeqPepTable.txt.gz 2020-06-13 15:32 12M
nestedRepeats.txt.gz 2020-06-12 18:23 18M
xenoRefSeqAli.txt.gz 2020-06-16 17:28 20M
simpleRepeat.txt.gz 2020-06-12 17:08 26M
chainHg38.txt.gz 2020-06-15 13:06 56M
chainMm10.txt.gz 2020-06-15 17:21 67M
netMm10.txt.gz 2020-06-15 17:28 75M
netMm39.txt.gz 2020-11-24 11:41 83M
chainMm39.txt.gz 2020-11-24 11:33 92M
rmsk.txt.gz 2020-06-12 18:21 139M
windowmaskerSdust.txt.gz 2020-06-12 19:56 145M
chainHg38Link.txt.gz 2020-06-15 13:07 164M
chainMm10Link.txt.gz 2020-06-15 17:25 524M
chainMm39Link.txt.gz 2020-11-24 11:37 557M