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 2.0K
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 2023-03-28 13:51 59K
trackDb.sql 2023-03-28 13:51 2.1K
tableList.txt.gz 2024-11-24 03:11 4.6K
tableList.sql 2024-11-24 03:11 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 8.0K
tableDescriptions.sql 2024-11-23 02:03 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 2023-03-28 13:51 970
hgFindSpec.sql 2023-03-28 13:51 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 2024-11-24 03:11 33
bigFiles.sql 2024-11-24 03:11 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