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 - all_est.sql 2016-06-05 12:13 2.1K all_est.txt.gz 2016-06-05 12:13 5.2M all_mrna.sql 2020-08-22 13:34 2.1K all_mrna.txt.gz 2020-08-22 13:34 73K augustusGene.sql 2015-07-26 17:05 1.9K augustusGene.txt.gz 2015-07-26 17:05 2.8M bigFiles.sql 2021-05-09 03:09 1.4K bigFiles.txt.gz 2021-05-09 03:09 68 chainMm10.sql 2012-11-21 15:56 1.7K chainMm10.txt.gz 2012-11-21 15:56 6.2M chainMm10Link.sql 2012-11-21 15:56 1.5K chainMm10Link.txt.gz 2012-11-21 15:56 50M chromAlias.sql 2018-02-18 07:44 1.4K chromAlias.txt.gz 2018-02-18 07:44 62K chromInfo.sql 2012-11-21 15:53 1.4K chromInfo.txt.gz 2012-11-21 15:53 27K cpgIslandExt.sql 2012-11-21 15:53 1.7K cpgIslandExt.txt.gz 2012-11-21 15:53 298K cpgIslandExtUnmasked.sql 2014-06-01 17:30 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:30 426K cytoBandIdeo.sql 2013-04-28 19:28 1.5K cytoBandIdeo.txt.gz 2013-04-28 19:28 25K estOrientInfo.sql 2016-06-05 12:13 1.8K estOrientInfo.txt.gz 2016-06-05 12:13 1.6M gap.sql 2012-11-21 15:56 1.6K gap.txt.gz 2012-11-21 15:56 957K gbLoaded.sql 2020-08-22 14:19 1.6K gbLoaded.txt.gz 2020-08-22 14:19 42K gc5BaseBw.sql 2012-11-21 15:55 1.3K gc5BaseBw.txt.gz 2012-11-21 15:55 63 genscan.sql 2012-11-21 15:54 1.7K genscan.txt.gz 2012-11-21 15:54 1.9M gold.sql 2012-11-21 15:53 1.7K gold.txt.gz 2012-11-21 15:53 600K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2021-01-21 09:36 1.8K hgFindSpec.txt.gz 2021-01-21 09:36 694 history.sql 2012-11-21 15:55 1.6K history.txt.gz 2012-11-21 15:55 505 intronEst.sql 2016-06-05 12:13 2.1K intronEst.txt.gz 2016-06-05 12:13 2.4M microsat.sql 2015-08-23 22:32 1.5K microsat.txt.gz 2015-08-23 22:32 252K mrnaOrientInfo.sql 2020-08-22 13:34 1.8K mrnaOrientInfo.txt.gz 2020-08-22 13:34 19K nestedRepeats.sql 2012-11-21 15:53 1.9K nestedRepeats.txt.gz 2012-11-21 15:53 233K netMm10.sql 2012-11-21 15:56 2.1K netMm10.txt.gz 2012-11-21 15:56 5.7M refFlat.sql 2020-08-22 13:52 1.7K refFlat.txt.gz 2020-08-22 13:52 16K refGene.sql 2020-08-22 13:52 1.9K refGene.txt.gz 2020-08-22 13:52 17K refSeqAli.sql 2020-03-01 08:05 2.1K refSeqAli.txt.gz 2020-03-01 08:05 19K rmsk.sql 2012-11-21 15:55 1.9K rmsk.txt.gz 2012-11-21 15:55 8.4M simpleRepeat.sql 2012-11-21 15:53 1.9K simpleRepeat.txt.gz 2012-11-21 15:53 4.0M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.1K tableList.sql 2021-05-09 03:09 1.6K tableList.txt.gz 2021-05-09 03:09 2.4K trackDb.sql 2021-01-21 09:35 2.1K trackDb.txt.gz 2021-01-21 09:35 39K ucscToINSDC.sql 2013-09-15 17:11 1.4K ucscToINSDC.txt.gz 2013-09-15 17:11 39K ucscToRefSeq.sql 2018-02-18 07:44 1.4K ucscToRefSeq.txt.gz 2018-02-18 07:44 39K windowmaskerSdust.sql 2012-11-21 15:53 1.5K windowmaskerSdust.txt.gz 2012-11-21 15:53 47M xenoRefFlat.sql 2020-08-22 14:19 1.7K xenoRefFlat.txt.gz 2020-08-22 14:19 30M xenoRefGene.sql 2020-08-22 14:19 1.9K xenoRefGene.txt.gz 2020-08-22 14:19 33M xenoRefSeqAli.sql 2020-08-22 14:19 2.1K xenoRefSeqAli.txt.gz 2020-08-22 14:19 29M