This directory contains a dump of the UCSC genome annotation database for
the Feb. 2011 (WTSI Devil_ref v7.0/sarHar1) assembly of the tasmanian devil genome (sarHar1, Wellcome Trust Sanger Institute Devil_ref v7.0 (GCA_000189315.1)).
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/3066
http://www.ncbi.nlm.nih.gov/genome/assembly/328478
http://www.ncbi.nlm.nih.gov/bioproject/51853
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=sarHar1
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/sarHar1/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/sarHar1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/sarHar1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sarHar1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sarHar1/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 sarHar1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql sarHar1 --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 -
windowmaskerSdust.sql 2012-07-11 20:49 1.5K
windowmaskerSdust.txt.gz 2012-07-11 20:49 203M
chainMm10Link.sql 2012-07-11 20:50 1.5K
chainMm10Link.txt.gz 2012-07-11 20:50 496M
gold.sql 2012-07-11 20:53 1.7K
chainMm10.sql 2012-07-11 20:53 1.7K
gold.txt.gz 2012-07-11 20:53 3.9M
history.sql 2012-07-11 20:53 1.6K
history.txt.gz 2012-07-11 20:53 406
chainMm10.txt.gz 2012-07-11 20:53 53M
genscan.sql 2012-07-11 20:53 1.7K
genscan.txt.gz 2012-07-11 20:53 1.6M
netMm10.sql 2012-07-11 20:53 2.1K
netMm10.txt.gz 2012-07-11 20:53 21M
gc5BaseBw.sql 2012-07-11 20:53 1.3K
gc5BaseBw.txt.gz 2012-07-11 20:53 63
cpgIslandExt.sql 2012-07-11 20:53 1.7K
cpgIslandExt.txt.gz 2012-07-11 20:53 453K
nestedRepeats.sql 2012-07-11 20:53 1.9K
nestedRepeats.txt.gz 2012-07-11 20:53 15M
chromInfo.sql 2012-07-11 20:53 1.4K
chromInfo.txt.gz 2012-07-11 20:53 204K
genscanPep.sql 2012-07-11 20:53 1.3K
genscanPep.txt.gz 2012-07-11 20:53 5.0M
gap.sql 2012-07-11 20:54 1.6K
gap.txt.gz 2012-07-11 20:54 2.6M
simpleRepeat.sql 2012-07-11 20:54 1.9K
simpleRepeat.txt.gz 2012-07-11 20:54 31M
rmsk.sql 2012-07-11 20:56 1.9K
rmsk.txt.gz 2012-07-11 20:56 166M
genscanSubopt.sql 2012-07-11 20:56 1.6K
genscanSubopt.txt.gz 2012-07-11 20:56 4.5M
cytoBandIdeo.sql 2013-04-28 21:47 1.5K
cytoBandIdeo.txt.gz 2013-04-28 21:47 207K
chainHg19Link.sql 2013-08-18 03:47 1.5K
chainHg19Link.txt.gz 2013-08-18 03:47 347M
netHg19.sql 2013-08-18 03:49 2.1K
netHg19.txt.gz 2013-08-18 03:49 19M
chainHg19.sql 2013-08-18 03:49 1.7K
chainHg19.txt.gz 2013-08-18 03:49 95M
ucscToINSDC.sql 2013-09-15 19:25 1.4K
ucscToINSDC.txt.gz 2013-09-15 19:25 280K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 19:47 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:47 516K
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 1.5M
microsat.sql 2015-08-24 01:40 1.5K
microsat.txt.gz 2015-08-24 01:40 1.0M
xenoMrna.sql 2016-02-28 06:44 2.1K
xenoMrna.txt.gz 2016-02-28 06:44 241M
refSeqAli.sql 2016-05-15 11:31 2.1K
refSeqAli.txt.gz 2016-05-15 11:31 2.8K
mrnaOrientInfo.sql 2017-06-19 13:49 1.8K
mrnaOrientInfo.txt.gz 2017-06-19 13:49 2.8K
all_mrna.sql 2017-06-19 13:51 2.1K
all_mrna.txt.gz 2017-06-19 13:51 5.7K
chromAlias.sql 2018-02-18 08:37 1.4K
chromAlias.txt.gz 2018-02-18 08:37 346K
ucscToRefSeq.sql 2018-02-18 08:37 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:37 280K
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:29 90
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:29 2.3M
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 202K
ncbiRefSeqCurated.sql 2020-05-10 03:29 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 2.8K
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 1.0M
ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75
ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 7.6M
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.3M
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 2.7M
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 497K
refGene.sql 2020-08-20 10:32 1.9K
refGene.txt.gz 2020-08-20 10:32 2.8K
refFlat.sql 2020-08-20 10:36 1.7K
refFlat.txt.gz 2020-08-20 10:36 2.6K
xenoRefGene.sql 2020-08-20 10:36 2.0K
xenoRefGene.txt.gz 2020-08-20 10:36 35M
xenoRefFlat.sql 2020-08-20 10:36 1.7K
xenoRefFlat.txt.gz 2020-08-20 10:36 31M
xenoRefSeqAli.sql 2020-08-20 10:49 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 10:49 32M
gbLoaded.sql 2020-08-20 10:49 1.6K
gbLoaded.txt.gz 2020-08-20 10:49 15K
ensGene.sql 2020-08-31 15:57 1.9K
ensGene.txt.gz 2020-08-31 15:57 2.0M
ensGtp.sql 2020-08-31 15:57 1.4K
ensGtp.txt.gz 2020-08-31 15:57 226K
ensemblToGeneName.sql 2020-08-31 15:57 1.4K
ensemblToGeneName.txt.gz 2020-08-31 15:57 95K
ensemblSource.sql 2020-08-31 18:30 1.4K
ensemblSource.txt.gz 2020-08-31 18:30 60K
ensPep.sql 2020-08-31 18:57 1.3K
ensPep.txt.gz 2020-08-31 18:57 5.7M
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 29K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.2K
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.5K
tableList.sql 2024-12-08 03:34 1.6K
tableList.txt.gz 2024-12-08 03:34 3.1K
bigFiles.sql 2024-12-08 03:34 1.4K
bigFiles.txt.gz 2024-12-08 03:34 94