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
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[   ]chr1.fa.gz10-Nov-2008 14:24 9.4M 
[   ]chr2.fa.gz10-Nov-2008 14:24 6.0M 
[   ]chr3.fa.gz10-Nov-2008 14:24 10M 
[   ]chr4.fa.gz10-Nov-2008 14:24 9.6M 
[   ]chr5.fa.gz10-Nov-2008 14:24 9.1M 
[   ]chr6.fa.gz10-Nov-2008 14:24 7.7M 
[   ]chr7.fa.gz10-Nov-2008 14:24 8.3M 
[   ]chr8.fa.gz10-Nov-2008 14:24 7.1M 
[   ]chr9.fa.gz10-Nov-2008 14:24 9.1M 
[   ]chr10.fa.gz10-Nov-2008 14:24 7.6M 
[   ]chr11.fa.gz10-Nov-2008 14:24 7.6M 
[   ]chr12.fa.gz10-Nov-2008 14:24 8.1M 
[   ]chr13.fa.gz10-Nov-2008 14:24 9.4M 
[   ]chr14.fa.gz10-Nov-2008 14:24 8.0M 
[   ]chr15.fa.gz10-Nov-2008 14:24 8.0M 
[   ]chr16.fa.gz10-Nov-2008 14:24 8.3M 
[   ]chr17.fa.gz10-Nov-2008 14:24 8.8M 
[   ]chr18.fa.gz10-Nov-2008 14:24 7.3M 
[   ]chr19.fa.gz10-Nov-2008 14:24 6.0M 
[   ]chr20.fa.gz10-Nov-2008 14:24 6.8M 
[   ]chr21.fa.gz10-Nov-2008 14:24 8.3M 
[   ]chr22.fa.gz10-Nov-2008 14:24 7.9M 
[   ]chr23.fa.gz10-Nov-2008 14:24 6.5M 
[   ]chr24.fa.gz10-Nov-2008 14:24 6.4M 
[   ]chrM.fa.gz10-Nov-2008 14:24 5.6K 
[TXT]md5sum.txt10-Nov-2008 14:35 1.2K 
[   ]scaffold.fa.tar.gz10-Nov-2008 14:30 27M 
[   ]ultracontig.fa.tar.gz10-Nov-2008 14:27 12M 

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