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 -
gc5BaseBw.txt.gz 2012-11-21 15:43 63
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
extNcbiRefSeq.txt.gz 2020-05-10 03:27 91
bigFiles.txt.gz 2024-11-17 03:37 94
grp.txt.gz 2014-03-02 03:40 208
history.txt.gz 2012-11-21 15:41 511
mrnaOrientInfo.txt.gz 2018-04-01 05:53 682
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
gc5BaseBw.sql 2012-11-21 15:43 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ensPep.sql 2021-05-25 14:32 1.3K
grp.sql 2014-03-02 03:40 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ensemblSource.sql 2021-05-25 14:32 1.4K
bigFiles.sql 2024-11-17 03:37 1.4K
chromInfo.sql 2012-11-21 15:46 1.4K
ensemblToGeneName.sql 2021-05-25 14:28 1.4K
chromAlias.sql 2018-02-18 06:14 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToINSDC.sql 2013-09-15 11:04 1.4K
ucscToRefSeq.sql 2018-02-18 06:14 1.4K
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
ensGtp.sql 2021-05-25 14:28 1.4K
microsat.sql 2015-08-23 13:40 1.5K
windowmaskerSdust.sql 2012-11-21 15:44 1.5K
cytoBandIdeo.sql 2013-04-28 12:59 1.5K
chainHg38Link.sql 2018-01-07 07:07 1.5K
chainMm10Link.sql 2012-11-21 15:34 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
tableList.sql 2024-11-17 03:37 1.6K
history.sql 2012-11-21 15:41 1.6K
gap.sql 2012-11-21 15:48 1.6K
gbLoaded.sql 2020-08-18 22:48 1.6K
gold.sql 2012-11-21 15:49 1.7K
genscan.sql 2012-11-21 15:41 1.7K
cpgIslandExt.sql 2012-11-21 15:48 1.7K
chainHg38.sql 2018-01-07 07:05 1.7K
chainMm10.sql 2012-11-21 15:39 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 11:04 1.7K
xenoRefFlat.sql 2020-08-18 22:45 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
mrnaOrientInfo.sql 2018-04-01 05:53 1.8K
rmsk.sql 2012-11-21 15:40 1.9K
simpleRepeat.sql 2012-11-21 15:48 1.9K
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
nestedRepeats.sql 2012-11-21 15:44 1.9K
augustusGene.sql 2015-07-26 12:00 1.9K
ensGene.sql 2021-05-25 14:28 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
xenoRefGene.sql 2020-08-18 22:45 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netHg38.sql 2018-01-07 07:07 2.1K
netMm10.sql 2012-11-21 15:41 2.1K
all_mrna.sql 2018-04-01 05:56 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
xenoMrna.sql 2020-08-18 22:31 2.1K
xenoRefSeqAli.sql 2020-08-18 22:48 2.1K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 2.2K
all_mrna.txt.gz 2018-04-01 05:56 2.9K
tableList.txt.gz 2024-11-17 03:37 3.0K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
gbLoaded.txt.gz 2020-08-18 22:48 34K
trackDb.txt.gz 2024-01-31 15:13 44K
microsat.txt.gz 2015-08-23 13:40 98K
ensemblSource.txt.gz 2021-05-25 14:32 112K
ensemblToGeneName.txt.gz 2021-05-25 14:28 136K
cytoBandIdeo.txt.gz 2013-04-28 12:59 246K
chromInfo.txt.gz 2012-11-21 15:46 251K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 261K
ucscToINSDC.txt.gz 2013-09-15 11:04 361K
ucscToRefSeq.txt.gz 2018-02-18 06:14 370K
ensGtp.txt.gz 2021-05-25 14:28 380K
chromAlias.txt.gz 2018-02-18 06:14 474K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 690K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.3M
cpgIslandExt.txt.gz 2012-11-21 15:48 1.6M
augustusGene.txt.gz 2015-07-26 12:00 2.4M
ensGene.txt.gz 2021-05-25 14:28 2.5M
cpgIslandExtUnmasked.txt.gz 2014-06-01 11:04 2.7M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 2.7M
ncbiRefSeq.txt.gz 2020-05-10 03:27 2.7M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 3.2M
gap.txt.gz 2012-11-21 15:48 3.3M
genscan.txt.gz 2012-11-21 15:41 3.7M
gold.txt.gz 2012-11-21 15:49 4.7M
ensPep.txt.gz 2021-05-25 14:32 7.6M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 8.3M
nestedRepeats.txt.gz 2012-11-21 15:44 17M
simpleRepeat.txt.gz 2012-11-21 15:48 18M
xenoRefFlat.txt.gz 2020-08-18 22:45 39M
xenoRefGene.txt.gz 2020-08-18 22:45 43M
xenoRefSeqAli.txt.gz 2020-08-18 22:48 46M
netMm10.txt.gz 2012-11-21 15:41 53M
netHg38.txt.gz 2018-01-07 07:07 61M
chainMm10.txt.gz 2012-11-21 15:40 115M
rmsk.txt.gz 2012-11-21 15:40 135M
windowmaskerSdust.txt.gz 2012-11-21 15:45 174M
chainHg38.txt.gz 2018-01-07 07:05 392M
xenoMrna.txt.gz 2020-08-18 22:31 429M
chainMm10Link.txt.gz 2012-11-21 15:36 711M
chainHg38Link.txt.gz 2018-01-07 07:09 1.4G