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
      Name                         Last modified      Size  Description
Parent Directory - chainDanRer7Link.txt.gz 2011-06-19 12:28 299M chainGasAcu1Link.txt.gz 2008-11-07 03:10 264M xenoMrna.txt.gz 2020-08-19 23:41 195M chainFr3Link.txt.gz 2012-05-28 11:58 189M chainTetNig2Link.txt.gz 2010-03-14 13:55 129M chainPetMar2Link.txt.gz 2013-01-24 04:26 100M chainDanRer7.txt.gz 2011-06-19 12:27 74M chainHg19Link.txt.gz 2009-10-11 08:40 62M windowmaskerSdust.txt.gz 2008-11-07 03:09 43M chainMm10Link.txt.gz 2013-10-27 19:34 43M chainGasAcu1.txt.gz 2008-11-07 03:15 37M chainGalGal6Link.txt.gz 2019-01-20 20:20 35M chainFr3.txt.gz 2012-05-28 12:02 33M all_est.txt.gz 2016-05-15 10:58 24M xenoRefGene.txt.gz 2020-08-19 23:59 23M multiz5way.txt.gz 2008-11-07 03:08 22M chainTetNig2.txt.gz 2010-03-14 13:55 21M xenoRefFlat.txt.gz 2020-08-19 23:59 21M chainPetMar2.txt.gz 2013-01-24 04:25 20M xenoRefSeqAli.txt.gz 2020-08-19 23:59 19M intronEst.txt.gz 2016-05-15 10:58 18M quality.txt.gz 2008-11-07 03:08 17M netGasAcu1.txt.gz 2008-11-07 03:14 17M netFr3.txt.gz 2012-05-28 11:56 16M netTetNig2.txt.gz 2010-03-14 13:56 15M phastCons5way.txt.gz 2008-11-07 03:15 13M chainHg19.txt.gz 2009-10-11 08:40 13M multiz5wayFrames.txt.gz 2008-11-07 03:19 13M netDanRer7.txt.gz 2011-06-19 12:27 13M phastConsElements5way.txt.gz 2008-11-07 03:08 9.4M chainMm10.txt.gz 2013-10-27 19:34 7.3M chainGalGal6.txt.gz 2019-01-20 20:20 6.9M estOrientInfo.txt.gz 2016-05-15 10:58 6.6M netGalGal6.txt.gz 2019-01-20 20:21 6.0M rmsk.txt.gz 2008-11-07 03:14 5.9M ensPep.txt.gz 2018-08-05 08:35 5.9M netHg19.txt.gz 2009-10-11 08:41 5.6M netMm10.txt.gz 2013-10-27 19:34 5.3M netPetMar2.txt.gz 2013-01-24 04:25 4.5M multiz5waySummary.txt.gz 2008-11-07 03:15 4.2M simpleRepeat.txt.gz 2008-11-07 03:18 3.9M gc5Base.txt.gz 2008-11-07 03:09 3.4M blastHg18KG.txt.gz 2009-12-20 15:24 2.9M augustusGene.txt.gz 2015-07-26 17:21 2.7M ensGene.txt.gz 2018-08-05 08:35 2.1M gold.txt.gz 2008-11-07 03:21 2.1M genscan.txt.gz 2013-12-10 03:35 1.7M gap.txt.gz 2008-11-07 03:08 1.5M ensGtp.txt.gz 2018-08-05 08:35 237K nestedRepeats.txt.gz 2008-11-07 03:08 221K ensemblToGeneName.txt.gz 2018-08-05 08:35 127K all_mrna.txt.gz 2020-08-19 23:41 111K pubsBlatPsl.txt.gz 2012-05-09 06:36 83K refSeqAli.txt.gz 2020-08-19 23:59 77K pubsBingBlat.txt.gz 2014-01-26 16:39 75K refGene.txt.gz 2020-08-19 23:59 71K ensemblSource.txt.gz 2018-08-05 08:35 70K refFlat.txt.gz 2020-08-19 23:59 64K pubsBlat.txt.gz 2012-05-09 06:36 58K trackDb.txt.gz 2021-12-27 12:23 56K gbLoaded.txt.gz 2020-08-19 23:59 42K pubsBingBlatPsl.txt.gz 2014-01-26 16:39 41K mrnaOrientInfo.txt.gz 2020-08-19 23:59 37K cytoBandIdeo.txt.gz 2013-04-28 19:47 35K chromInfo.txt.gz 2008-11-07 03:08 35K chromAlias.txt.gz 2018-08-05 08:36 34K microsat.txt.gz 2008-11-07 03:15 27K ctgPos2.txt.gz 2008-11-07 03:14 18K tRNAs.txt.gz 2012-04-16 03:39 16K tableDescriptions.txt.gz 2019-07-21 03:43 7.8K tableList.txt.gz 2022-10-02 03:05 4.5K pubsBingBlat.sql 2014-01-26 16:39 2.4K netHg19.sql 2009-10-11 08:41 2.3K blastHg18KG.sql 2009-12-20 15:24 2.3K netGasAcu1.sql 2008-11-07 03:14 2.2K pubsBingBlatPsl.sql 2014-01-26 16:39 2.2K xenoRefSeqAli.sql 2020-08-19 23:59 2.1K refSeqAli.sql 2020-08-19 23:59 2.1K intronEst.sql 2016-05-15 10:58 2.1K xenoMrna.sql 2020-08-19 23:41 2.1K all_mrna.sql 2020-08-19 23:41 2.1K all_est.sql 2016-05-15 10:58 2.1K netPetMar2.sql 2013-01-24 04:25 2.1K netGalGal6.sql 2019-01-20 20:21 2.1K pubsBlatPsl.sql 2012-05-09 06:36 2.1K netMm10.sql 2013-10-27 19:34 2.1K trackDb.sql 2021-12-27 12:23 2.1K netTetNig2.sql 2010-03-14 13:56 2.0K netDanRer7.sql 2011-06-19 12:27 2.0K netFr3.sql 2012-05-28 11:56 2.0K augustusGene.sql 2015-07-26 17:21 1.9K xenoRefGene.sql 2020-08-19 23:59 1.9K refGene.sql 2020-08-19 23:59 1.9K ensGene.sql 2018-08-05 08:35 1.9K simpleRepeat.sql 2008-11-07 03:18 1.9K nestedRepeats.sql 2008-11-07 03:08 1.9K pubsBlat.sql 2012-05-09 06:36 1.9K rmsk.sql 2008-11-07 03:14 1.9K mrnaOrientInfo.sql 2020-08-19 23:59 1.8K chainHg19.sql 2009-10-11 08:40 1.8K estOrientInfo.sql 2016-05-15 10:58 1.8K hgFindSpec.sql 2021-12-27 12:23 1.8K phastCons5way.sql 2008-11-07 03:14 1.7K xenoRefFlat.sql 2020-08-19 23:59 1.7K quality.sql 2008-11-07 03:08 1.7K gc5Base.sql 2008-11-07 03:09 1.7K chainPetMar2.sql 2013-01-24 04:25 1.7K chainGalGal6.sql 2019-01-20 20:20 1.7K refFlat.sql 2020-08-19 23:59 1.7K chainMm10.sql 2013-10-27 19:34 1.7K tRNAs.sql 2012-04-16 03:39 1.7K genscan.sql 2013-12-10 03:35 1.7K multiz5wayFrames.sql 2008-11-07 03:19 1.7K chainGasAcu1.sql 2008-11-07 03:15 1.7K chainTetNig2.sql 2010-03-14 13:55 1.6K chainDanRer7.sql 2011-06-19 12:27 1.6K chainFr3.sql 2012-05-28 12:02 1.6K gold.sql 2008-11-07 03:21 1.6K gbLoaded.sql 2020-08-19 23:59 1.6K tableList.sql 2022-10-02 03:05 1.6K chainPetMar2Link.sql 2013-01-24 04:25 1.6K chainGalGal6Link.sql 2019-01-20 20:20 1.5K chainMm10Link.sql 2013-10-27 19:34 1.5K chainHg19Link.sql 2009-10-11 08:40 1.5K cytoBandIdeo.sql 2013-04-28 19:47 1.5K gap.sql 2008-11-07 03:08 1.5K chainTetNig2Link.sql 2010-03-14 13:55 1.5K chainDanRer7Link.sql 2011-06-19 12:28 1.5K chainFr3Link.sql 2012-05-28 11:56 1.5K multiz5waySummary.sql 2008-11-07 03:15 1.5K phastConsElements5way.sql 2008-11-07 03:08 1.4K history.sql 2008-11-07 03:14 1.4K chromAlias.sql 2018-08-05 08:36 1.4K ensGtp.sql 2018-08-05 08:35 1.4K chainGasAcu1Link.sql 2008-11-07 03:09 1.4K multiz5way.sql 2008-11-07 03:07 1.4K ctgPos2.sql 2008-11-07 03:14 1.4K tableDescriptions.sql 2019-07-21 03:43 1.4K ensemblToGeneName.sql 2018-08-05 08:35 1.4K grp.sql 2014-03-02 04:14 1.4K windowmaskerSdust.sql 2008-11-07 03:09 1.4K bigFiles.sql 2022-10-02 03:05 1.4K ensemblSource.sql 2018-08-05 08:35 1.4K microsat.sql 2008-11-07 03:15 1.3K ensPep.sql 2018-08-05 08:35 1.3K extFile.sql 2008-11-07 03:18 1.3K chromInfo.sql 2008-11-07 03:08 1.2K history.txt.gz 2008-11-07 03:14 927 hgFindSpec.txt.gz 2021-12-27 12:23 918 grp.txt.gz 2014-03-02 04:14 209 extFile.txt.gz 2008-11-07 03:18 104 bigFiles.txt.gz 2022-10-02 03:05 33