This directory contains a dump of the UCSC genome annotation database for
the Dec. 2011 (Baylor/dasNov3) assembly of the armadillo genome (dasNov3, Baylor College of Medicine Dasnov3.0 (GCA_000208655.2)).
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/235
http://www.ncbi.nlm.nih.gov/genome/assembly/326198
http://www.ncbi.nlm.nih.gov/bioproject/12594
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=dasNov3
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/dasNov3/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/dasNov3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/dasNov3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/dasNov3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/dasNov3/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 dasNov3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql dasNov3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
For conditions of use regarding the Armadillo genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use
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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.
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Name Last modified Size Description
Parent Directory -
all_mrna.sql 15-Aug-2016 12:27 2.1K
all_mrna.txt.gz 15-Aug-2016 12:27 1.8K
augustusGene.sql 26-Jul-2015 12:00 1.9K
augustusGene.txt.gz 26-Jul-2015 12:00 2.4M
bigFiles.sql 09-Jul-2017 08:34 1.4K
bigFiles.txt.gz 09-Jul-2017 08:34 68
chainMm10.sql 21-Nov-2012 15:39 1.7K
chainMm10.txt.gz 21-Nov-2012 15:40 115M
chainMm10Link.sql 21-Nov-2012 15:34 1.5K
chainMm10Link.txt.gz 21-Nov-2012 15:36 711M
chromInfo.sql 21-Nov-2012 15:46 1.4K
chromInfo.txt.gz 21-Nov-2012 15:46 251K
cpgIslandExt.sql 21-Nov-2012 15:48 1.7K
cpgIslandExt.txt.gz 21-Nov-2012 15:48 1.6M
cpgIslandExtUnmasked.sql 01-Jun-2014 11:04 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 11:04 2.7M
cytoBandIdeo.sql 28-Apr-2013 12:59 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 12:59 246K
ensGene.sql 20-Nov-2016 06:41 1.9K
ensGene.txt.gz 20-Nov-2016 06:41 2.5M
ensGtp.sql 20-Nov-2016 06:40 1.4K
ensGtp.txt.gz 20-Nov-2016 06:40 380K
ensPep.sql 20-Nov-2016 06:37 1.3K
ensPep.txt.gz 20-Nov-2016 06:37 7.6M
ensemblSource.sql 20-Nov-2016 06:41 1.4K
ensemblSource.txt.gz 20-Nov-2016 06:41 112K
ensemblToGeneName.sql 20-Nov-2016 06:41 1.4K
ensemblToGeneName.txt.gz 20-Nov-2016 06:41 124K
gap.sql 21-Nov-2012 15:48 1.6K
gap.txt.gz 21-Nov-2012 15:48 3.3M
gbLoaded.sql 09-Jul-2017 08:35 1.6K
gbLoaded.txt.gz 09-Jul-2017 08:35 24K
gc5BaseBw.sql 21-Nov-2012 15:43 1.3K
gc5BaseBw.txt.gz 21-Nov-2012 15:43 63
genscan.sql 21-Nov-2012 15:41 1.7K
genscan.txt.gz 21-Nov-2012 15:41 3.7M
gold.sql 21-Nov-2012 15:49 1.7K
gold.txt.gz 21-Nov-2012 15:49 4.7M
grp.sql 02-Mar-2014 03:40 1.3K
grp.txt.gz 02-Mar-2014 03:40 208
hgFindSpec.sql 09-Jul-2017 08:35 1.7K
hgFindSpec.txt.gz 09-Jul-2017 08:35 686
history.sql 21-Nov-2012 15:41 1.6K
history.txt.gz 21-Nov-2012 15:41 511
microsat.sql 23-Aug-2015 13:40 1.5K
microsat.txt.gz 23-Aug-2015 13:40 98K
mrnaOrientInfo.sql 15-Aug-2016 12:27 1.8K
mrnaOrientInfo.txt.gz 15-Aug-2016 12:27 520
nestedRepeats.sql 21-Nov-2012 15:44 1.9K
nestedRepeats.txt.gz 21-Nov-2012 15:44 17M
netMm10.sql 21-Nov-2012 15:41 2.1K
netMm10.txt.gz 21-Nov-2012 15:41 53M
rmsk.sql 21-Nov-2012 15:40 1.9K
rmsk.txt.gz 21-Nov-2012 15:40 135M
simpleRepeat.sql 21-Nov-2012 15:48 1.9K
simpleRepeat.txt.gz 21-Nov-2012 15:48 18M
tableDescriptions.sql 09-Jul-2017 08:34 1.4K
tableDescriptions.txt.gz 09-Jul-2017 08:34 4.3K
tableList.sql 09-Jul-2017 08:35 1.5K
tableList.txt.gz 09-Jul-2017 08:35 2.2K
trackDb.sql 09-Jul-2017 08:34 2.0K
trackDb.txt.gz 09-Jul-2017 08:34 25K
ucscToINSDC.sql 15-Sep-2013 11:04 1.4K
ucscToINSDC.txt.gz 15-Sep-2013 11:04 361K
windowmaskerSdust.sql 21-Nov-2012 15:44 1.5K
windowmaskerSdust.txt.gz 21-Nov-2012 15:45 174M
xenoMrna.sql 09-Jul-2017 08:35 2.1K
xenoMrna.txt.gz 09-Jul-2017 08:37 374M
xenoRefFlat.sql 09-Jul-2017 08:39 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 08:39 34M
xenoRefGene.sql 09-Jul-2017 08:35 1.9K
xenoRefGene.txt.gz 09-Jul-2017 08:35 38M
xenoRefSeqAli.sql 09-Jul-2017 08:34 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 08:34 38M