This directory contains the Oct. 2005 assembly of the medaka genome
(oryLat2, MEDAKA1), as well as repeat annotations and GenBank sequences.
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:
oryLat2.2bit - contains the complete medaka/oryLat2 genome sequence
in the 2bit file format. 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. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
oryLat2.agp.gz - Description of how the assembly was generated from
oryLat2.fa.gz - "Soft-masked" assembly sequence in one file.
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.
oryLat2.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
oryLat2.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
RepeatMasker version: October 6, 2006 (open-3-1-6)
with RepBase libraries: RepBase Update 20061006.
oryLat2.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
est.fa.gz - Medaka ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
oryLat2.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Medaka mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
ensGene.upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for Ensembl genes with annotated 5' UTRs.
This file is updated with each new release of Ensembl genes.
ensGene.upstream2000.fa.gz - Same as upstream1000, but 2000 bases.
ensGene.upstream5000.fa.gz - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
oryLat2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/oryLat2/bigZips. 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/bigZips/ .
For a single file, e.g. chromFa.tar.gz
Or with wget, all files:
With wget, a single file:
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
Please note the Medaka genome data release policy:
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
Finally, we are continuing to improve the assembly; therefore, any feedback
information on the assembly from the users should be highly welcomed.
Contact information: firstname.lastname@example.org
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80