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