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