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