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 found at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ See also: http://genome.ucsc.edu/admin/git.html http://genome.ucsc.edu/admin/jk-install.html oryLat2.agp.gz - Description of how the assembly was generated from fragments. 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 upper case. 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 format. 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 updates. 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 GenBank updates. oryLat2.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. oryLat2.chromAlias.txt - sequence name alias file, one line for each sequence name. First column is sequence name followed by tab separated alias names. ------------------------------------------------------------------ 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 ... - 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 rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf .tar.gz To uncompress the fa.gz files: gunzip .fa.gz ______________________________________________________________________ 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