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.
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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 -
chainRn6Link.txt.gz 2017-03-27 18:55 630M
chainNeoSch1Link.txt.gz 2020-07-16 17:54 316M
rmsk.txt.gz 2016-02-08 14:05 127M
chainRn6.txt.gz 2017-03-27 18:43 123M
windowmaskerSdust.txt.gz 2016-02-08 14:05 90M
chainNeoSch1.txt.gz 2020-07-16 17:52 54M
xenoRefGene.txt.gz 2020-08-19 23:14 35M
xenoRefSeqAli.txt.gz 2020-08-19 23:14 34M
xenoRefFlat.txt.gz 2020-08-19 23:14 31M
netNeoSch1.txt.gz 2020-07-16 17:56 21M
simpleRepeat.txt.gz 2016-02-08 14:05 18M
netRn6.txt.gz 2017-03-27 19:16 17M
nestedRepeats.txt.gz 2016-02-08 14:04 12M
gold.txt.gz 2016-02-08 14:04 6.0M
ensPep.txt.gz 2019-02-10 03:42 4.9M
genscanSubopt.txt.gz 2016-02-08 14:04 4.7M
chromAlias.txt.gz 2017-09-03 05:42 3.4M
gap.txt.gz 2016-02-08 14:04 2.8M
genscan.txt.gz 2016-02-08 14:05 2.7M
cpgIslandExtUnmasked.txt.gz 2016-02-08 14:04 2.4M
ensGene.txt.gz 2019-02-10 03:42 2.0M
augustusGene.txt.gz 2016-02-08 14:04 1.9M
cpgIslandExt.txt.gz 2016-02-08 14:04 1.7M
all_est.txt.gz 2016-02-08 14:04 1.6M
ucscToINSDC.txt.gz 2016-02-08 14:05 1.5M
cytoBandIdeo.txt.gz 2016-02-08 14:04 1.0M
chromInfo.txt.gz 2016-02-08 14:04 1.0M
estOrientInfo.txt.gz 2016-02-08 14:04 542K
ensGtp.txt.gz 2019-02-10 03:42 323K
intronEst.txt.gz 2016-02-08 14:04 203K
microsat.txt.gz 2016-02-08 14:04 100K
ensemblSource.txt.gz 2019-02-10 03:42 95K
ensemblToGeneName.txt.gz 2019-02-10 03:42 72K
gbLoaded.txt.gz 2020-08-19 23:14 46K
trackDb.txt.gz 2023-03-28 13:51 41K
refSeqAli.txt.gz 2020-03-01 08:08 24K
refGene.txt.gz 2020-08-19 22:55 22K
refFlat.txt.gz 2020-08-19 22:55 20K
all_mrna.txt.gz 2018-04-01 07:40 15K
mrnaOrientInfo.txt.gz 2020-03-01 08:09 14K
tableDescriptions.txt.gz 2024-11-16 02:03 5.4K
tableList.txt.gz 2024-11-17 03:20 2.7K
xenoRefSeqAli.sql 2020-08-19 23:14 2.1K
netNeoSch1.sql 2020-07-16 17:56 2.1K
refSeqAli.sql 2020-03-01 08:08 2.1K
intronEst.sql 2016-02-08 14:04 2.1K
all_mrna.sql 2018-04-01 07:40 2.1K
all_est.sql 2016-02-08 14:04 2.1K
netRn6.sql 2017-03-27 19:15 2.1K
trackDb.sql 2023-03-28 13:51 2.1K
xenoRefGene.sql 2020-08-19 23:14 2.0K
refGene.sql 2020-08-19 22:55 1.9K
augustusGene.sql 2016-02-08 14:04 1.9K
nestedRepeats.sql 2016-02-08 14:04 1.9K
simpleRepeat.sql 2016-02-08 14:05 1.9K
ensGene.sql 2019-02-10 03:42 1.9K
rmsk.sql 2016-02-08 14:05 1.9K
mrnaOrientInfo.sql 2020-03-01 08:09 1.8K
estOrientInfo.sql 2016-02-08 14:04 1.8K
hgFindSpec.sql 2023-03-28 13:51 1.8K
xenoRefFlat.sql 2020-08-19 23:14 1.7K
chainNeoSch1.sql 2020-07-16 17:52 1.7K
refFlat.sql 2020-08-19 22:55 1.7K
cpgIslandExtUnmasked.sql 2016-02-08 14:04 1.7K
chainRn6.sql 2017-03-27 18:41 1.7K
cpgIslandExt.sql 2016-02-08 14:04 1.7K
genscan.sql 2016-02-08 14:05 1.7K
gold.sql 2016-02-08 14:04 1.7K
gbLoaded.sql 2020-08-19 23:14 1.6K
gap.sql 2016-02-08 14:04 1.6K
history.sql 2016-02-08 14:04 1.6K
chainNeoSch1Link.sql 2020-07-16 17:54 1.6K
genscanSubopt.sql 2016-02-08 14:04 1.6K
tableList.sql 2024-11-17 03:20 1.6K
chainRn6Link.sql 2017-03-27 18:47 1.5K
cytoBandIdeo.sql 2016-02-08 14:04 1.5K
windowmaskerSdust.sql 2016-02-08 14:05 1.5K
microsat.sql 2016-02-08 14:04 1.5K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToINSDC.sql 2016-02-08 14:05 1.4K
chromAlias.sql 2017-09-03 05:42 1.4K
ensGtp.sql 2019-02-10 03:42 1.4K
chromInfo.sql 2016-02-08 14:04 1.4K
ensemblToGeneName.sql 2019-02-10 03:42 1.4K
bigFiles.sql 2024-11-17 03:20 1.4K
ensemblSource.sql 2019-02-10 03:42 1.4K
grp.sql 2016-02-08 14:04 1.3K
ensPep.sql 2019-02-10 03:42 1.3K
gc5BaseBw.sql 2016-02-08 14:05 1.3K
hgFindSpec.txt.gz 2023-03-28 13:51 856
history.txt.gz 2016-02-08 14:04 421
grp.txt.gz 2016-02-08 14:04 213
bigFiles.txt.gz 2024-11-17 03:20 69
gc5BaseBw.txt.gz 2016-02-08 14:05 66