This directory contains a dump of the UCSC genome annotation database for the
Jan. 2018 (Susie_PABv2/ponAbe3) assembly of the orangutan genome
(ponAbe3, 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/325
https://www.ncbi.nlm.nih.gov/genome/assembly/1529631
https://www.ncbi.nlm.nih.gov/bioproject/369439
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=ponAbe3
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/ponAbe3/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/ponAbe3/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/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 ponAbe3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ponAbe3 --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 -
gc5BaseBw.txt.gz 2018-11-01 17:05 66
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
bigFiles.txt.gz 2025-11-09 14:05 95
grp.txt.gz 2018-11-01 17:05 213
history.txt.gz 2018-11-01 17:01 853
hgFindSpec.txt.gz 2025-06-11 11:58 1.2K
gc5BaseBw.sql 2018-11-01 17:05 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
grp.sql 2018-11-01 17:05 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
chromInfo.sql 2018-11-01 17:05 1.4K
bigFiles.sql 2025-11-09 14:05 1.4K
chromAlias.sql 2018-11-01 17:05 1.4K
ucscToINSDC.sql 2018-11-01 17:06 1.4K
ucscToRefSeq.sql 2018-11-01 17:06 1.4K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
tableDescriptions.sql 2025-11-09 09:24 1.5K
microsat.sql 2018-11-01 17:06 1.5K
windowmaskerSdust.sql 2018-11-01 17:06 1.5K
cytoBandIdeo.sql 2018-11-01 17:05 1.5K
chainHg38Link.sql 2018-11-01 17:01 1.5K
chainMm10Link.sql 2018-11-01 17:02 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
history.sql 2018-11-01 17:01 1.6K
tableList.sql 2025-11-09 14:05 1.6K
gap.sql 2018-11-01 17:05 1.6K
gold.sql 2018-11-01 17:06 1.7K
genscan.sql 2018-11-01 17:06 1.7K
cpgIslandExt.sql 2018-11-01 17:05 1.7K
chainHg38.sql 2018-11-01 17:01 1.7K
chainMm10.sql 2018-11-01 17:02 1.7K
refFlat.sql 2018-11-01 17:05 1.7K
cpgIslandExtUnmasked.sql 2018-11-01 17:05 1.7K
xenoRefFlat.sql 2018-11-01 17:06 1.7K
estOrientInfo.sql 2018-11-01 17:05 1.8K
mrnaOrientInfo.sql 2018-11-01 17:06 1.8K
hgFindSpec.sql 2025-06-11 11:58 1.8K
rmsk.sql 2018-11-01 17:05 1.9K
refGene.sql 2018-11-01 17:05 1.9K
simpleRepeat.sql 2018-11-01 17:06 1.9K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
nestedRepeats.sql 2018-11-01 17:00 1.9K
xenoRefGene.sql 2018-11-01 17:06 1.9K
augustusGene.sql 2018-11-01 17:00 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
trackDb.sql 2025-06-11 11:58 2.1K
netHg38.sql 2018-11-01 17:00 2.1K
netMm10.sql 2018-11-01 17:01 2.1K
all_est.sql 2018-11-01 17:00 2.1K
all_mrna.sql 2018-11-01 17:00 2.1K
intronEst.sql 2018-11-01 17:06 2.1K
refSeqAli.sql 2018-11-01 17:05 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
xenoRefSeqAli.sql 2018-11-01 17:07 2.1K
tableList.txt.gz 2025-11-09 14:05 3.0K
tableDescriptions.txt.gz 2025-11-09 09:24 6.1K
gap.txt.gz 2018-11-01 17:05 8.7K
cytoBandIdeo.txt.gz 2018-11-01 17:05 33K
chromInfo.txt.gz 2018-11-01 17:05 36K
ucscToRefSeq.txt.gz 2018-11-01 17:06 47K
ucscToINSDC.txt.gz 2018-11-01 17:06 51K
chromAlias.txt.gz 2018-11-01 17:05 54K
trackDb.txt.gz 2025-06-11 11:58 65K
gold.txt.gz 2018-11-01 17:06 80K
mrnaOrientInfo.txt.gz 2018-11-01 17:06 150K
microsat.txt.gz 2018-11-01 17:06 239K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 338K
refFlat.txt.gz 2018-11-01 17:05 359K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 366K
refGene.txt.gz 2018-11-01 17:05 385K
refSeqAli.txt.gz 2018-11-01 17:05 398K
all_mrna.txt.gz 2018-11-01 17:00 531K
cpgIslandExt.txt.gz 2018-11-01 17:05 591K
estOrientInfo.txt.gz 2018-11-01 17:05 648K
cpgIslandExtUnmasked.txt.gz 2018-11-01 17:05 862K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 881K
intronEst.txt.gz 2018-11-01 17:06 1.3M
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M
all_est.txt.gz 2018-11-01 17:00 2.1M
augustusGene.txt.gz 2018-11-01 17:00 2.3M
genscan.txt.gz 2018-11-01 17:06 2.8M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.1M
ncbiRefSeq.txt.gz 2020-05-10 03:28 3.3M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 9.3M
netHg38.txt.gz 2018-11-01 17:01 11M
nestedRepeats.txt.gz 2018-11-01 17:00 18M
xenoRefSeqAli.txt.gz 2018-11-01 17:07 20M
xenoRefFlat.txt.gz 2018-11-01 17:06 20M
xenoRefGene.txt.gz 2018-11-01 17:06 22M
chainHg38.txt.gz 2018-11-01 17:01 23M
simpleRepeat.txt.gz 2018-11-01 17:06 28M
chainMm10.txt.gz 2018-11-01 17:02 60M
netMm10.txt.gz 2018-11-01 17:02 72M
rmsk.txt.gz 2018-11-01 17:05 141M
windowmaskerSdust.txt.gz 2018-11-01 17:06 146M
chainHg38Link.txt.gz 2018-11-01 17:01 157M
chainMm10Link.txt.gz 2018-11-01 17:03 503M