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 -
multiz5way.sql 2008-11-07 03:07 1.4K
multiz5way.txt.gz 2008-11-07 03:08 22M
gap.sql 2008-11-07 03:08 1.5K
gap.txt.gz 2008-11-07 03:08 1.5M
nestedRepeats.sql 2008-11-07 03:08 1.9K
nestedRepeats.txt.gz 2008-11-07 03:08 221K
phastConsElements5way.sql 2008-11-07 03:08 1.4K
phastConsElements5way.txt.gz 2008-11-07 03:08 9.4M
chromInfo.sql 2008-11-07 03:08 1.2K
chromInfo.txt.gz 2008-11-07 03:08 35K
quality.sql 2008-11-07 03:08 1.7K
quality.txt.gz 2008-11-07 03:08 17M
windowmaskerSdust.sql 2008-11-07 03:09 1.4K
windowmaskerSdust.txt.gz 2008-11-07 03:09 43M
gc5Base.sql 2008-11-07 03:09 1.7K
gc5Base.txt.gz 2008-11-07 03:09 3.4M
chainGasAcu1Link.sql 2008-11-07 03:09 1.4K
chainGasAcu1Link.txt.gz 2008-11-07 03:10 264M
ctgPos2.sql 2008-11-07 03:14 1.4K
ctgPos2.txt.gz 2008-11-07 03:14 18K
netGasAcu1.sql 2008-11-07 03:14 2.2K
netGasAcu1.txt.gz 2008-11-07 03:14 17M
rmsk.sql 2008-11-07 03:14 1.9K
rmsk.txt.gz 2008-11-07 03:14 5.9M
history.sql 2008-11-07 03:14 1.4K
history.txt.gz 2008-11-07 03:14 927
phastCons5way.sql 2008-11-07 03:14 1.7K
phastCons5way.txt.gz 2008-11-07 03:15 13M
chainGasAcu1.sql 2008-11-07 03:15 1.7K
chainGasAcu1.txt.gz 2008-11-07 03:15 37M
microsat.sql 2008-11-07 03:15 1.3K
microsat.txt.gz 2008-11-07 03:15 27K
multiz5waySummary.sql 2008-11-07 03:15 1.5K
multiz5waySummary.txt.gz 2008-11-07 03:15 4.2M
simpleRepeat.sql 2008-11-07 03:18 1.9K
simpleRepeat.txt.gz 2008-11-07 03:18 3.9M
extFile.sql 2008-11-07 03:18 1.3K
extFile.txt.gz 2008-11-07 03:18 104
multiz5wayFrames.sql 2008-11-07 03:19 1.7K
multiz5wayFrames.txt.gz 2008-11-07 03:19 13M
gold.sql 2008-11-07 03:21 1.6K
gold.txt.gz 2008-11-07 03:21 2.1M
chainHg19Link.sql 2009-10-11 08:40 1.5K
chainHg19Link.txt.gz 2009-10-11 08:40 62M
chainHg19.sql 2009-10-11 08:40 1.8K
chainHg19.txt.gz 2009-10-11 08:40 13M
netHg19.sql 2009-10-11 08:41 2.3K
netHg19.txt.gz 2009-10-11 08:41 5.6M
blastHg18KG.sql 2009-12-20 15:24 2.3K
blastHg18KG.txt.gz 2009-12-20 15:24 2.9M
chainTetNig2.sql 2010-03-14 13:55 1.6K
chainTetNig2.txt.gz 2010-03-14 13:55 21M
chainTetNig2Link.sql 2010-03-14 13:55 1.5K
chainTetNig2Link.txt.gz 2010-03-14 13:55 129M
netTetNig2.sql 2010-03-14 13:56 2.0K
netTetNig2.txt.gz 2010-03-14 13:56 15M
chainDanRer7.sql 2011-06-19 12:27 1.6K
chainDanRer7.txt.gz 2011-06-19 12:27 74M
netDanRer7.sql 2011-06-19 12:27 2.0K
netDanRer7.txt.gz 2011-06-19 12:27 13M
chainDanRer7Link.sql 2011-06-19 12:28 1.5K
chainDanRer7Link.txt.gz 2011-06-19 12:28 299M
tRNAs.sql 2012-04-16 03:39 1.7K
tRNAs.txt.gz 2012-04-16 03:39 16K
pubsBlat.sql 2012-05-09 06:36 1.9K
pubsBlat.txt.gz 2012-05-09 06:36 58K
pubsBlatPsl.sql 2012-05-09 06:36 2.1K
pubsBlatPsl.txt.gz 2012-05-09 06:36 83K
netFr3.sql 2012-05-28 11:56 2.0K
netFr3.txt.gz 2012-05-28 11:56 16M
chainFr3Link.sql 2012-05-28 11:56 1.5K
chainFr3Link.txt.gz 2012-05-28 11:58 189M
chainFr3.sql 2012-05-28 12:02 1.6K
chainFr3.txt.gz 2012-05-28 12:02 33M
netPetMar2.sql 2013-01-24 04:25 2.1K
netPetMar2.txt.gz 2013-01-24 04:25 4.5M
chainPetMar2.sql 2013-01-24 04:25 1.7K
chainPetMar2.txt.gz 2013-01-24 04:25 20M
chainPetMar2Link.sql 2013-01-24 04:25 1.6K
chainPetMar2Link.txt.gz 2013-01-24 04:26 100M
cytoBandIdeo.sql 2013-04-28 19:47 1.5K
cytoBandIdeo.txt.gz 2013-04-28 19:47 35K
netMm10.sql 2013-10-27 19:34 2.1K
netMm10.txt.gz 2013-10-27 19:34 5.3M
chainMm10.sql 2013-10-27 19:34 1.7K
chainMm10.txt.gz 2013-10-27 19:34 7.3M
chainMm10Link.sql 2013-10-27 19:34 1.5K
chainMm10Link.txt.gz 2013-10-27 19:34 43M
genscan.sql 2013-12-10 03:35 1.7K
genscan.txt.gz 2013-12-10 03:35 1.7M
pubsBingBlat.sql 2014-01-26 16:39 2.4K
pubsBingBlat.txt.gz 2014-01-26 16:39 75K
pubsBingBlatPsl.sql 2014-01-26 16:39 2.2K
pubsBingBlatPsl.txt.gz 2014-01-26 16:39 41K
grp.sql 2014-03-02 04:14 1.4K
grp.txt.gz 2014-03-02 04:14 209
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.7M
all_est.sql 2016-05-15 10:58 2.1K
all_est.txt.gz 2016-05-15 10:58 24M
estOrientInfo.sql 2016-05-15 10:58 1.8K
estOrientInfo.txt.gz 2016-05-15 10:58 6.6M
intronEst.sql 2016-05-15 10:58 2.1K
intronEst.txt.gz 2016-05-15 10:58 18M
ensGene.sql 2018-08-05 08:35 1.9K
ensGene.txt.gz 2018-08-05 08:35 2.1M
ensPep.sql 2018-08-05 08:35 1.3K
ensPep.txt.gz 2018-08-05 08:35 5.9M
ensGtp.sql 2018-08-05 08:35 1.4K
ensGtp.txt.gz 2018-08-05 08:35 237K
ensemblSource.sql 2018-08-05 08:35 1.4K
ensemblSource.txt.gz 2018-08-05 08:35 70K
ensemblToGeneName.sql 2018-08-05 08:35 1.4K
ensemblToGeneName.txt.gz 2018-08-05 08:35 127K
chromAlias.sql 2018-08-05 08:36 1.4K
chromAlias.txt.gz 2018-08-05 08:36 34K
chainGalGal6.sql 2019-01-20 20:20 1.7K
chainGalGal6.txt.gz 2019-01-20 20:20 6.9M
chainGalGal6Link.sql 2019-01-20 20:20 1.5K
chainGalGal6Link.txt.gz 2019-01-20 20:20 35M
netGalGal6.sql 2019-01-20 20:21 2.1K
netGalGal6.txt.gz 2019-01-20 20:21 6.0M
all_mrna.sql 2020-08-19 23:41 2.1K
all_mrna.txt.gz 2020-08-19 23:41 111K
xenoMrna.sql 2020-08-19 23:41 2.1K
xenoMrna.txt.gz 2020-08-19 23:41 195M
refGene.sql 2020-08-19 23:59 1.9K
refGene.txt.gz 2020-08-19 23:59 71K
refFlat.sql 2020-08-19 23:59 1.7K
refFlat.txt.gz 2020-08-19 23:59 64K
xenoRefGene.sql 2020-08-19 23:59 2.0K
xenoRefGene.txt.gz 2020-08-19 23:59 23M
xenoRefFlat.sql 2020-08-19 23:59 1.7K
xenoRefFlat.txt.gz 2020-08-19 23:59 21M
mrnaOrientInfo.sql 2020-08-19 23:59 1.8K
mrnaOrientInfo.txt.gz 2020-08-19 23:59 37K
refSeqAli.sql 2020-08-19 23:59 2.1K
refSeqAli.txt.gz 2020-08-19 23:59 77K
xenoRefSeqAli.sql 2020-08-19 23:59 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 23:59 19M
gbLoaded.sql 2020-08-19 23:59 1.6K
gbLoaded.txt.gz 2020-08-19 23:59 42K
trackDb.sql 2023-03-28 13:51 2.1K
trackDb.txt.gz 2023-03-28 13:51 59K
hgFindSpec.sql 2023-03-28 13:51 1.8K
hgFindSpec.txt.gz 2023-03-28 13:51 970
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 8.0K
tableList.sql 2024-11-17 03:20 1.6K
tableList.txt.gz 2024-11-17 03:20 4.6K
bigFiles.sql 2024-11-17 03:20 1.4K
bigFiles.txt.gz 2024-11-17 03:20 33