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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
all_est.sql 2018-11-01 17:00 2.1K
all_est.txt.gz 2018-11-01 17:00 2.1M
nestedRepeats.sql 2018-11-01 17:00 1.9K
nestedRepeats.txt.gz 2018-11-01 17:00 18M
all_mrna.sql 2018-11-01 17:00 2.1K
all_mrna.txt.gz 2018-11-01 17:00 531K
augustusGene.sql 2018-11-01 17:00 1.9K
augustusGene.txt.gz 2018-11-01 17:00 2.3M
netHg38.sql 2018-11-01 17:00 2.1K
netHg38.txt.gz 2018-11-01 17:01 11M
chainHg38.sql 2018-11-01 17:01 1.7K
chainHg38.txt.gz 2018-11-01 17:01 23M
chainHg38Link.sql 2018-11-01 17:01 1.5K
history.sql 2018-11-01 17:01 1.6K
history.txt.gz 2018-11-01 17:01 853
chainHg38Link.txt.gz 2018-11-01 17:01 157M
netMm10.sql 2018-11-01 17:01 2.1K
netMm10.txt.gz 2018-11-01 17:02 72M
chainMm10.sql 2018-11-01 17:02 1.7K
chainMm10.txt.gz 2018-11-01 17:02 60M
chainMm10Link.sql 2018-11-01 17:02 1.5K
chainMm10Link.txt.gz 2018-11-01 17:03 503M
chromAlias.sql 2018-11-01 17:05 1.4K
chromAlias.txt.gz 2018-11-01 17:05 54K
chromInfo.sql 2018-11-01 17:05 1.4K
chromInfo.txt.gz 2018-11-01 17:05 36K
cpgIslandExt.sql 2018-11-01 17:05 1.7K
cpgIslandExt.txt.gz 2018-11-01 17:05 591K
cpgIslandExtUnmasked.sql 2018-11-01 17:05 1.7K
cpgIslandExtUnmasked.txt.gz 2018-11-01 17:05 862K
cytoBandIdeo.sql 2018-11-01 17:05 1.5K
cytoBandIdeo.txt.gz 2018-11-01 17:05 33K
grp.sql 2018-11-01 17:05 1.3K
grp.txt.gz 2018-11-01 17:05 213
refFlat.sql 2018-11-01 17:05 1.7K
refFlat.txt.gz 2018-11-01 17:05 359K
estOrientInfo.sql 2018-11-01 17:05 1.8K
estOrientInfo.txt.gz 2018-11-01 17:05 648K
gap.sql 2018-11-01 17:05 1.6K
gap.txt.gz 2018-11-01 17:05 8.7K
gc5BaseBw.sql 2018-11-01 17:05 1.3K
gc5BaseBw.txt.gz 2018-11-01 17:05 66
refGene.sql 2018-11-01 17:05 1.9K
refGene.txt.gz 2018-11-01 17:05 385K
refSeqAli.sql 2018-11-01 17:05 2.1K
refSeqAli.txt.gz 2018-11-01 17:05 398K
rmsk.sql 2018-11-01 17:05 1.9K
rmsk.txt.gz 2018-11-01 17:05 141M
genscan.sql 2018-11-01 17:06 1.7K
genscan.txt.gz 2018-11-01 17:06 2.8M
gold.sql 2018-11-01 17:06 1.7K
gold.txt.gz 2018-11-01 17:06 80K
intronEst.sql 2018-11-01 17:06 2.1K
intronEst.txt.gz 2018-11-01 17:06 1.3M
simpleRepeat.sql 2018-11-01 17:06 1.9K
simpleRepeat.txt.gz 2018-11-01 17:06 28M
microsat.sql 2018-11-01 17:06 1.5K
microsat.txt.gz 2018-11-01 17:06 239K
mrnaOrientInfo.sql 2018-11-01 17:06 1.8K
mrnaOrientInfo.txt.gz 2018-11-01 17:06 150K
ucscToINSDC.sql 2018-11-01 17:06 1.4K
ucscToINSDC.txt.gz 2018-11-01 17:06 51K
ucscToRefSeq.sql 2018-11-01 17:06 1.4K
ucscToRefSeq.txt.gz 2018-11-01 17:06 47K
windowmaskerSdust.sql 2018-11-01 17:06 1.5K
windowmaskerSdust.txt.gz 2018-11-01 17:06 146M
xenoRefFlat.sql 2018-11-01 17:06 1.7K
xenoRefFlat.txt.gz 2018-11-01 17:06 20M
xenoRefGene.sql 2018-11-01 17:06 1.9K
xenoRefGene.txt.gz 2018-11-01 17:06 22M
xenoRefSeqAli.sql 2018-11-01 17:07 2.1K
xenoRefSeqAli.txt.gz 2018-11-01 17:07 20M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.2M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 3.3M
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 338K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 366K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.6M
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 9.3M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 881K
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.1M
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 64K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.1K
tableDescriptions.sql 2024-11-02 02:04 1.5K
tableDescriptions.txt.gz 2024-11-02 02:04 6.1K
tableList.sql 2024-11-03 03:05 1.6K
tableList.txt.gz 2024-11-03 03:05 3.0K
bigFiles.sql 2024-11-03 03:05 1.4K
bigFiles.txt.gz 2024-11-03 03:05 95