This directory contains a dump of the UCSC genome annotation database for the
Feb. 2007 (ASM227v2/ornAna2) assembly of the platypus genome
(ornAna2, WUGSC ASM227v2) .
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/110
http://www.ncbi.nlm.nih.gov/genome/assembly/237598
http://www.ncbi.nlm.nih.gov/bioproject/19039
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=ornAna2
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/ornAna2/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/ornAna2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ornAna2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ornAna2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ornAna2/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 ornAna2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ornAna2 --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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-19 23:14 34M
xenoRefSeqAli.sql 2020-08-19 23:14 2.1K
xenoRefGene.txt.gz 2020-08-19 23:14 35M
xenoRefGene.sql 2020-08-19 23:14 2.0K
xenoRefFlat.txt.gz 2020-08-19 23:14 31M
xenoRefFlat.sql 2020-08-19 23:14 1.7K
windowmaskerSdust.txt.gz 2016-02-08 14:05 90M
windowmaskerSdust.sql 2016-02-08 14:05 1.5K
ucscToINSDC.txt.gz 2016-02-08 14:05 1.5M
ucscToINSDC.sql 2016-02-08 14:05 1.4K
trackDb.txt.gz 2023-03-28 13:51 41K
trackDb.sql 2023-03-28 13:51 2.1K
tableList.txt.gz 2024-11-17 03:20 2.7K
tableList.sql 2024-11-17 03:20 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 5.4K
tableDescriptions.sql 2024-11-16 02:03 1.5K
simpleRepeat.txt.gz 2016-02-08 14:05 18M
simpleRepeat.sql 2016-02-08 14:05 1.9K
rmsk.txt.gz 2016-02-08 14:05 127M
rmsk.sql 2016-02-08 14:05 1.9K
refSeqAli.txt.gz 2020-03-01 08:08 24K
refSeqAli.sql 2020-03-01 08:08 2.1K
refGene.txt.gz 2020-08-19 22:55 22K
refGene.sql 2020-08-19 22:55 1.9K
refFlat.txt.gz 2020-08-19 22:55 20K
refFlat.sql 2020-08-19 22:55 1.7K
netRn6.txt.gz 2017-03-27 19:16 17M
netRn6.sql 2017-03-27 19:15 2.1K
netNeoSch1.txt.gz 2020-07-16 17:56 21M
netNeoSch1.sql 2020-07-16 17:56 2.1K
nestedRepeats.txt.gz 2016-02-08 14:04 12M
nestedRepeats.sql 2016-02-08 14:04 1.9K
mrnaOrientInfo.txt.gz 2020-03-01 08:09 14K
mrnaOrientInfo.sql 2020-03-01 08:09 1.8K
microsat.txt.gz 2016-02-08 14:04 100K
microsat.sql 2016-02-08 14:04 1.5K
intronEst.txt.gz 2016-02-08 14:04 203K
intronEst.sql 2016-02-08 14:04 2.1K
history.txt.gz 2016-02-08 14:04 421
history.sql 2016-02-08 14:04 1.6K
hgFindSpec.txt.gz 2023-03-28 13:51 856
hgFindSpec.sql 2023-03-28 13:51 1.8K
grp.txt.gz 2016-02-08 14:04 213
grp.sql 2016-02-08 14:04 1.3K
gold.txt.gz 2016-02-08 14:04 6.0M
gold.sql 2016-02-08 14:04 1.7K
genscanSubopt.txt.gz 2016-02-08 14:04 4.7M
genscanSubopt.sql 2016-02-08 14:04 1.6K
genscan.txt.gz 2016-02-08 14:05 2.7M
genscan.sql 2016-02-08 14:05 1.7K
gc5BaseBw.txt.gz 2016-02-08 14:05 66
gc5BaseBw.sql 2016-02-08 14:05 1.3K
gbLoaded.txt.gz 2020-08-19 23:14 46K
gbLoaded.sql 2020-08-19 23:14 1.6K
gap.txt.gz 2016-02-08 14:04 2.8M
gap.sql 2016-02-08 14:04 1.6K
estOrientInfo.txt.gz 2016-02-08 14:04 542K
estOrientInfo.sql 2016-02-08 14:04 1.8K
ensemblToGeneName.txt.gz 2019-02-10 03:42 72K
ensemblToGeneName.sql 2019-02-10 03:42 1.4K
ensemblSource.txt.gz 2019-02-10 03:42 95K
ensemblSource.sql 2019-02-10 03:42 1.4K
ensPep.txt.gz 2019-02-10 03:42 4.9M
ensPep.sql 2019-02-10 03:42 1.3K
ensGtp.txt.gz 2019-02-10 03:42 323K
ensGtp.sql 2019-02-10 03:42 1.4K
ensGene.txt.gz 2019-02-10 03:42 2.0M
ensGene.sql 2019-02-10 03:42 1.9K
cytoBandIdeo.txt.gz 2016-02-08 14:04 1.0M
cytoBandIdeo.sql 2016-02-08 14:04 1.5K
cpgIslandExtUnmasked.txt.gz 2016-02-08 14:04 2.4M
cpgIslandExtUnmasked.sql 2016-02-08 14:04 1.7K
cpgIslandExt.txt.gz 2016-02-08 14:04 1.7M
cpgIslandExt.sql 2016-02-08 14:04 1.7K
chromInfo.txt.gz 2016-02-08 14:04 1.0M
chromInfo.sql 2016-02-08 14:04 1.4K
chromAlias.txt.gz 2017-09-03 05:42 3.4M
chromAlias.sql 2017-09-03 05:42 1.4K
chainRn6Link.txt.gz 2017-03-27 18:55 630M
chainRn6Link.sql 2017-03-27 18:47 1.5K
chainRn6.txt.gz 2017-03-27 18:43 123M
chainRn6.sql 2017-03-27 18:41 1.7K
chainNeoSch1Link.txt.gz 2020-07-16 17:54 316M
chainNeoSch1Link.sql 2020-07-16 17:54 1.6K
chainNeoSch1.txt.gz 2020-07-16 17:52 54M
chainNeoSch1.sql 2020-07-16 17:52 1.7K
bigFiles.txt.gz 2024-11-17 03:20 69
bigFiles.sql 2024-11-17 03:20 1.4K
augustusGene.txt.gz 2016-02-08 14:04 1.9M
augustusGene.sql 2016-02-08 14:04 1.9K
all_mrna.txt.gz 2018-04-01 07:40 15K
all_mrna.sql 2018-04-01 07:40 2.1K
all_est.txt.gz 2016-02-08 14:04 1.6M
all_est.sql 2016-02-08 14:04 2.1K