This directory contains a dump of the UCSC genome annotation database for the
Oct. 2013 (KORDI BalAcu1.0/balAcu1) assembly of the minke whale genome
(balAcu1, KORDI BalAcu1.0 (GCA_000493695.1))
from the Genome Sequencing Consortium.
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/10769
http://www.ncbi.nlm.nih.gov/genome/assembly/78761
http://www.ncbi.nlm.nih.gov/bioproject/237330
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=balAcu1
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/balAcu1/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/balAcu1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/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 balAcu1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql balAcu1 --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 -
nestedRepeats.sql 2014-04-11 15:17 1.9K
nestedRepeats.txt.gz 2014-04-11 15:17 11M
chromInfo.sql 2014-04-11 15:17 1.4K
chromInfo.txt.gz 2014-04-11 15:17 41K
cpgIslandExt.sql 2014-04-11 15:17 1.7K
cpgIslandExt.txt.gz 2014-04-11 15:17 959K
genscan.sql 2014-04-11 15:17 1.7K
genscan.txt.gz 2014-04-11 15:17 2.9M
cpgIslandExtUnmasked.sql 2014-04-11 15:17 1.7K
cpgIslandExtUnmasked.txt.gz 2014-04-11 15:17 1.3M
cytoBandIdeo.sql 2014-04-11 15:17 1.5K
cytoBandIdeo.txt.gz 2014-04-11 15:17 41K
history.sql 2014-04-11 15:17 1.6K
history.txt.gz 2014-04-11 15:17 404
gap.sql 2014-04-11 15:17 1.6K
gap.txt.gz 2014-04-11 15:17 2.2M
rmsk.sql 2014-04-11 15:17 1.9K
rmsk.txt.gz 2014-04-11 15:17 103M
simpleRepeat.sql 2014-04-11 15:18 1.9K
simpleRepeat.txt.gz 2014-04-11 15:18 16M
gc5BaseBw.sql 2014-04-11 15:18 1.3K
gc5BaseBw.txt.gz 2014-04-11 15:18 66
genscanSubopt.sql 2014-04-11 15:18 1.6K
genscanSubopt.txt.gz 2014-04-11 15:18 5.9M
gold.sql 2014-04-11 15:18 1.7K
gold.txt.gz 2014-04-11 15:18 3.0M
ucscToINSDC.sql 2014-04-11 15:18 1.4K
ucscToINSDC.txt.gz 2014-04-11 15:18 65K
windowmaskerSdust.sql 2014-04-11 15:18 1.5K
windowmaskerSdust.txt.gz 2014-04-11 15:18 123M
grp.sql 2014-10-19 07:13 1.3K
grp.txt.gz 2014-10-19 07:13 200
augustusGene.sql 2015-07-26 10:13 1.9K
augustusGene.txt.gz 2015-07-26 10:13 2.2M
microsat.sql 2015-08-23 09:56 1.5K
microsat.txt.gz 2015-08-23 09:56 291K
chromAlias.sql 2018-02-18 05:08 1.4K
chromAlias.txt.gz 2018-02-18 05:08 104K
ucscToRefSeq.sql 2018-02-18 05:08 1.4K
ucscToRefSeq.txt.gz 2018-02-18 05:08 67K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.7M
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.2M
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 252K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 619
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 7.2M
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 645K
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.7M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.3M
xenoRefGene.sql 2020-08-18 08:08 2.0K
xenoRefGene.txt.gz 2020-08-18 08:08 40M
xenoRefFlat.sql 2020-08-18 08:08 1.7K
xenoRefFlat.txt.gz 2020-08-18 08:08 36M
xenoRefSeqAli.sql 2020-08-18 08:08 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 08:08 41M
gbLoaded.sql 2020-08-18 08:08 1.6K
gbLoaded.txt.gz 2020-08-18 08:08 11K
trackDb_pushedout.sql 2023-12-05 13:53 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:53 18K
hgFindSpec_pushedout.sql 2023-12-05 13:53 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:53 1.0K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 33K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
tableDescriptions.sql 2024-04-20 02:03 1.5K
tableDescriptions.txt.gz 2024-04-20 02:03 5.2K
tableList.sql 2024-04-21 03:38 1.6K
tableList.txt.gz 2024-04-21 03:38 2.4K
bigFiles.sql 2024-04-21 03:38 1.4K
bigFiles.txt.gz 2024-04-21 03:38 95