This directory contains a dump of the UCSC genome annotation database for
the Jan. 2011 (Nile tilapia/oreNil2) assembly of the nile tilapia genome (oreNil2, Broad Institute of MIT and Harvard Orenil1.1 (GCA_000188235.1)).
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/197
http://www.ncbi.nlm.nih.gov/genome/assembly/354508
http://www.ncbi.nlm.nih.gov/bioproject/59571
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=oreNil2
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/oreNil2/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/oreNil2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/oreNil2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oreNil2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oreNil2/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 oreNil2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oreNil2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Nile tilapia sequence is made freely available before scientific publication
with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions if the provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
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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 -
simpleRepeat.sql 2012-11-21 15:53 1.9K
simpleRepeat.txt.gz 2012-11-21 15:53 4.0M
cpgIslandExt.sql 2012-11-21 15:53 1.7K
cpgIslandExt.txt.gz 2012-11-21 15:53 298K
gold.sql 2012-11-21 15:53 1.7K
gold.txt.gz 2012-11-21 15:53 600K
nestedRepeats.sql 2012-11-21 15:53 1.9K
nestedRepeats.txt.gz 2012-11-21 15:53 233K
chromInfo.sql 2012-11-21 15:53 1.4K
chromInfo.txt.gz 2012-11-21 15:53 27K
windowmaskerSdust.sql 2012-11-21 15:53 1.5K
windowmaskerSdust.txt.gz 2012-11-21 15:53 47M
genscan.sql 2012-11-21 15:54 1.7K
genscan.txt.gz 2012-11-21 15:54 1.9M
history.sql 2012-11-21 15:55 1.6K
history.txt.gz 2012-11-21 15:55 505
rmsk.sql 2012-11-21 15:55 1.9K
rmsk.txt.gz 2012-11-21 15:55 8.4M
gc5BaseBw.sql 2012-11-21 15:55 1.3K
gc5BaseBw.txt.gz 2012-11-21 15:55 63
chainMm10Link.sql 2012-11-21 15:56 1.5K
chainMm10Link.txt.gz 2012-11-21 15:56 50M
gap.sql 2012-11-21 15:56 1.6K
gap.txt.gz 2012-11-21 15:56 957K
chainMm10.sql 2012-11-21 15:56 1.7K
chainMm10.txt.gz 2012-11-21 15:56 6.2M
netMm10.sql 2012-11-21 15:56 2.1K
netMm10.txt.gz 2012-11-21 15:56 5.7M
cytoBandIdeo.sql 2013-04-28 19:28 1.5K
cytoBandIdeo.txt.gz 2013-04-28 19:28 25K
ucscToINSDC.sql 2013-09-15 17:11 1.4K
ucscToINSDC.txt.gz 2013-09-15 17:11 39K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 17:30 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:30 426K
augustusGene.sql 2015-07-26 17:05 1.9K
augustusGene.txt.gz 2015-07-26 17:05 2.8M
microsat.sql 2015-08-23 22:32 1.5K
microsat.txt.gz 2015-08-23 22:32 252K
all_est.sql 2016-06-05 12:13 2.1K
all_est.txt.gz 2016-06-05 12:13 5.2M
intronEst.sql 2016-06-05 12:13 2.1K
intronEst.txt.gz 2016-06-05 12:13 2.4M
estOrientInfo.sql 2016-06-05 12:13 1.8K
estOrientInfo.txt.gz 2016-06-05 12:13 1.6M
ncbiRefSeq.sql 2018-02-09 13:44 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:44 3.4M
ncbiRefSeqCurated.sql 2018-02-09 13:44 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:44 13K
ncbiRefSeqPredicted.sql 2018-02-09 13:44 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:44 3.4M
ncbiRefSeqLink.sql 2018-02-09 13:44 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:44 1.5M
ncbiRefSeqPsl.sql 2018-02-09 13:44 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:44 4.2M
ncbiRefSeqCds.sql 2018-02-09 14:18 1.4K
ncbiRefSeqCds.txt.gz 2018-02-09 14:18 330K
ncbiRefSeqOther.sql 2018-02-09 14:18 1.3K
ncbiRefSeqOther.txt.gz 2018-02-09 14:18 75
ncbiRefSeqPepTable.sql 2018-02-09 14:18 1.4K
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:18 11M
extNcbiRefSeq.sql 2018-02-09 14:18 1.5K
extNcbiRefSeq.txt.gz 2018-02-09 14:18 91
seqNcbiRefSeq.sql 2018-02-09 14:18 1.6K
seqNcbiRefSeq.txt.gz 2018-02-09 14:18 807K
chromAlias.sql 2018-02-18 07:44 1.4K
chromAlias.txt.gz 2018-02-18 07:44 62K
ucscToRefSeq.sql 2018-02-18 07:44 1.4K
ucscToRefSeq.txt.gz 2018-02-18 07:44 39K
refSeqAli.sql 2020-03-01 08:05 2.1K
refSeqAli.txt.gz 2020-03-01 08:05 19K
all_mrna.sql 2020-08-22 13:34 2.1K
all_mrna.txt.gz 2020-08-22 13:34 73K
mrnaOrientInfo.sql 2020-08-22 13:34 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 13:34 19K
refGene.sql 2020-08-22 13:52 1.9K
refGene.txt.gz 2020-08-22 13:52 17K
refFlat.sql 2020-08-22 13:52 1.7K
refFlat.txt.gz 2020-08-22 13:52 16K
xenoRefGene.sql 2020-08-22 14:19 2.0K
xenoRefGene.txt.gz 2020-08-22 14:19 33M
xenoRefFlat.sql 2020-08-22 14:19 1.7K
xenoRefFlat.txt.gz 2020-08-22 14:19 30M
xenoRefSeqAli.sql 2020-08-22 14:19 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 14:19 29M
gbLoaded.sql 2020-08-22 14:19 1.6K
gbLoaded.txt.gz 2020-08-22 14:19 42K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 61K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.2K
tableDescriptions.sql 2024-11-23 02:03 1.5K
tableDescriptions.txt.gz 2024-11-23 02:03 6.0K
tableList.sql 2024-11-24 03:32 1.6K
tableList.txt.gz 2024-11-24 03:32 3.0K
bigFiles.sql 2024-11-24 03:32 1.4K
bigFiles.txt.gz 2024-11-24 03:32 94