This directory contains a dump of the UCSC genome annotation database for the
Oct. 2011 (Baylor Ttru_1.4/turTru2) assembly of the dolphin genome (turTru2,
Baylor College of Medicine Ttru_1.4 (NCBI project 20365, GCA_000151865.2, WGS ABRN02)).
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/769
http://www.ncbi.nlm.nih.gov/genome/assembly/325108
http://www.ncbi.nlm.nih.gov/bioproject/20367
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=turTru2
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/turTru2/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/turTru2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/turTru2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/turTru2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/turTru2/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 turTru2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql turTru2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
For conditions of use regarding the Dolphin 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 -
augustusGene.sql 2019-01-03 13:30 1.9K
augustusGene.txt.gz 2019-01-03 13:30 2.1M
chainBosTau7.sql 2019-01-03 13:30 1.7K
chainBosTau7.txt.gz 2019-01-03 13:31 1.5G
chainBosTau7Link.sql 2019-01-03 13:36 1.5K
chainBosTau7Link.txt.gz 2019-01-03 13:42 4.4G
chainMm10.sql 2019-01-03 13:59 1.7K
chainMm10.txt.gz 2019-01-03 13:59 33M
chainMm10Link.sql 2019-01-03 13:59 1.5K
chainMm10Link.txt.gz 2019-01-03 13:59 326M
chromInfo.sql 2019-01-03 14:01 1.4K
chromInfo.txt.gz 2019-01-03 14:01 1.0M
cpgIslandExt.sql 2019-01-03 14:01 1.7K
cpgIslandExt.txt.gz 2019-01-03 14:01 966K
cpgIslandExtUnmasked.sql 2019-01-03 14:01 1.7K
cpgIslandExtUnmasked.txt.gz 2019-01-03 14:01 1.4M
cytoBandIdeo.sql 2019-01-03 14:01 1.5K
cytoBandIdeo.txt.gz 2019-01-03 14:01 1.0M
gap.sql 2019-01-03 14:01 1.6K
gap.txt.gz 2019-01-03 14:01 3.5M
gc5BaseBw.sql 2019-01-03 14:01 1.3K
gc5BaseBw.txt.gz 2019-01-03 14:01 63
genscan.sql 2019-01-03 14:01 1.7K
genscan.txt.gz 2019-01-03 14:01 2.9M
gold.sql 2019-01-03 14:01 1.7K
gold.txt.gz 2019-01-03 14:01 6.6M
grp.sql 2019-01-03 14:01 1.3K
grp.txt.gz 2019-01-03 14:01 208
history.sql 2019-01-03 14:01 1.6K
history.txt.gz 2019-01-03 14:01 561
microsat.sql 2019-01-03 14:01 1.5K
microsat.txt.gz 2019-01-03 14:01 458K
nestedRepeats.sql 2019-01-03 14:01 1.9K
nestedRepeats.txt.gz 2019-01-03 14:01 11M
netBosTau7.sql 2019-01-03 14:01 2.1K
netBosTau7.txt.gz 2019-01-03 14:01 61M
netMm10.sql 2019-01-03 14:01 2.1K
netMm10.txt.gz 2019-01-03 14:01 61M
rmsk.sql 2019-01-03 14:01 1.9K
rmsk.txt.gz 2019-01-03 14:01 106M
simpleRepeat.sql 2019-01-03 14:02 1.9K
simpleRepeat.txt.gz 2019-01-03 14:02 16M
ucscToINSDC.sql 2019-01-03 14:02 1.4K
ucscToINSDC.txt.gz 2019-01-03 14:02 1.6M
windowmaskerSdust.sql 2019-01-03 14:02 1.5K
windowmaskerSdust.txt.gz 2019-01-03 14:02 121M
xenoRefGene.sql 2020-08-20 17:29 2.0K
xenoRefGene.txt.gz 2020-08-20 17:29 38M
xenoRefFlat.sql 2020-08-20 17:29 1.7K
xenoRefFlat.txt.gz 2020-08-20 17:29 34M
xenoRefSeqAli.sql 2020-08-20 17:29 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 17:29 42M
gbLoaded.sql 2020-08-20 17:43 1.6K
gbLoaded.txt.gz 2020-08-20 17:43 14K
chainMm39.sql 2020-11-24 20:19 1.7K
chainMm39.txt.gz 2020-11-24 20:19 21M
chainMm39Link.sql 2020-11-24 20:21 1.6K
chainMm39Link.txt.gz 2020-11-24 20:21 291M
netMm39.sql 2020-11-24 20:24 2.1K
netMm39.txt.gz 2020-11-24 20:24 61M
trackDb.sql 2023-03-28 13:54 2.1K
trackDb.txt.gz 2023-03-28 13:54 35K
hgFindSpec.sql 2023-03-28 13:54 1.8K
hgFindSpec.txt.gz 2023-03-28 13:54 581
tableDescriptions.sql 2024-11-23 02:04 1.5K
tableDescriptions.txt.gz 2024-11-23 02:04 4.8K
tableList.sql 2024-11-24 03:32 1.6K
tableList.txt.gz 2024-11-24 03:32 2.1K
bigFiles.sql 2024-11-24 03:32 1.4K
bigFiles.txt.gz 2024-11-24 03:32 68