This directory contains the Oct. 2005 assembly of the medaka genome
(oryLat2, MEDAKA1). 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/"
chr*.fa.gz - "Soft-masked" assembly sequence for each chromosome.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
ultracontig.fa.tar.gz - sequence that has not been placed into chromosomes.
Soft-masked as explained above.
scaffold.fa.tar.gz - sequence that has not been placed into ultracontigs
or chromosomes. Soft-masked as explained above.
md5sum.txt - MD5 checksum of these files to verify correct transmission
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If you plan to download a large file or multiple files from this
directory, we recommend that 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/chromosomes. To download
multiple files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
To unpack the fa.gz files:
gunzip <file>.fa.gz
To unpack the fa.tar.gz files:
tar -xvzf <file>.fa.tar.gz
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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 -
md5sum.txt 2008-11-10 14:35 1.2K
chrM.fa.gz 2008-11-10 14:24 5.6K
chr2.fa.gz 2008-11-10 14:24 6.0M
chr19.fa.gz 2008-11-10 14:24 6.0M
chr24.fa.gz 2008-11-10 14:24 6.4M
chr23.fa.gz 2008-11-10 14:24 6.5M
chr20.fa.gz 2008-11-10 14:24 6.8M
chr8.fa.gz 2008-11-10 14:24 7.1M
chr18.fa.gz 2008-11-10 14:24 7.3M
chr11.fa.gz 2008-11-10 14:24 7.6M
chr10.fa.gz 2008-11-10 14:24 7.6M
chr6.fa.gz 2008-11-10 14:24 7.7M
chr22.fa.gz 2008-11-10 14:24 7.9M
chr14.fa.gz 2008-11-10 14:24 8.0M
chr15.fa.gz 2008-11-10 14:24 8.0M
chr12.fa.gz 2008-11-10 14:24 8.1M
chr21.fa.gz 2008-11-10 14:24 8.3M
chr7.fa.gz 2008-11-10 14:24 8.3M
chr16.fa.gz 2008-11-10 14:24 8.3M
chr17.fa.gz 2008-11-10 14:24 8.8M
chr5.fa.gz 2008-11-10 14:24 9.1M
chr9.fa.gz 2008-11-10 14:24 9.1M
chr13.fa.gz 2008-11-10 14:24 9.4M
chr1.fa.gz 2008-11-10 14:24 9.4M
chr4.fa.gz 2008-11-10 14:24 9.6M
chr3.fa.gz 2008-11-10 14:24 10M
ultracontig.fa.tar.gz 2008-11-10 14:27 12M
scaffold.fa.tar.gz 2008-11-10 14:30 27M