This directory contains a dump of the UCSC genome annotation database for
the Oct. 2005 assembly of the medaka genome (oryLat2, MEDAKA1).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by Institute of Genetics (NIG)
and the Morishita Laboratory, University of Tokyo.
For more information on the medaka genome, see the project websites:
NIG - http://dolphin.lab.nig.ac.jp/medaka/
Morishita Laboratory - http://medaka.utgenome.org/"

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=oryLat2
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

---------------------------------------------------------------
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/oryLat2/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/oryLat2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/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 oryLat2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oryLat2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

______________________________________________________________________
Please note the Medaka genome data release policy:
	http://medaka.utgenome.org/#policy

Quote:
    We (the medaka genome sequencing project) herein make the draft assembly of
    the medaka (Oryzias latipes) Hd-rR genome publicly available by providing
    genome browsing function before scientific publication. We reserve the
    exclusive right to publish, in a timely manner, the assembly and sequence of
    the medaka genome along with an initial genome-scale analysis. Reserved
    analyses include the identification of complete sets of genomic features 
    such as (predicted) genes, gene families, paralogues,regulatory elements,
    repeat structures, GC content, etc., and the identification of regions of
    evolutionary conservation across the entire genome.

    All users may search and use the draft assembly freely under the 
    restrictions of the previous paragraph. Since the current version is still
    a preliminary one and may contain mistakes, users should use the data at
    their own rish and are not allowed to redistribute or repackage the data.
    When users publish the analysis of individual genes and genomic regions
    using the data of this site, they should include the acknowledgement
    "The data has been provided freely by the National Institute of Genetics
    and the University of Tokyo for use in this
    publication/correspondence only."

    Finally, we are continuing to improve the assembly; therefore, any feedback
    information on the assembly from the users should be highly welcomed.

    Contact information: medaka@nematode.lab.nig.ac.jp