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 2024-04-21 03:14 33
extFile.txt.gz 2008-11-07 03:18 104
grp.txt.gz 2014-03-02 04:14 209
history.txt.gz 2008-11-07 03:14 927
hgFindSpec_pushedout.txt.gz 2021-12-27 12:23 928
hgFindSpec.txt.gz 2023-03-28 13:51 970
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
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
bigFiles.sql 2024-04-21 03:14 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
tableDescriptions.sql 2024-04-20 02:03 1.5K
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
gold.sql 2008-11-07 03:21 1.6K
tableList.sql 2024-04-21 03:14 1.6K
gbLoaded.sql 2020-08-19 23:59 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
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
refFlat.sql 2020-08-19 23:59 1.7K
phastCons5way.sql 2008-11-07 03:14 1.7K
xenoRefFlat.sql 2020-08-19 23:59 1.7K
hgFindSpec.sql 2023-03-28 13:51 1.8K
estOrientInfo.sql 2016-05-15 10:58 1.8K
chainHg19.sql 2009-10-11 08:40 1.8K
hgFindSpec_pushedout.sql 2021-12-27 12:23 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
augustusGene.sql 2015-07-26 17:21 1.9K
refGene.sql 2020-08-19 23:59 1.9K
xenoRefGene.sql 2020-08-19 23:59 2.0K
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 2023-03-28 13:51 2.1K
trackDb_pushedout.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
intronEst.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
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 2024-04-21 03:14 4.7K
tableDescriptions.txt.gz 2024-04-20 02:03 8.0K
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_pushedout.txt.gz 2021-12-27 12:23 56K
pubsBlat.txt.gz 2012-05-09 06:36 58K
trackDb.txt.gz 2023-03-28 13:51 59K
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