This directory contains the Mar. 2007 assembly of the tetraodon genome (tetNig2, Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000)), as well as repeat annotations and GenBank sequences. This assembly was produced by Genoscope - Centre National de Séquençage and the Broad Institute. For more information on the tetraodon genome, see the project website: http://www.genoscope.cns.fr/spip/ http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-a-fish-with.html http://www.broadinstitute.org/annotation/tetraodon/background.html Files included in this directory: tetNig2.2bit - contains the complete tetraodon/tetNig2 genome sequence in the 2bit file format. 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/cvs.html http://genome.ucsc.edu/admin/jk-install.html chromAgp.tar.gz - Description of how the assembly was generated from fragments, unpacking to one file per chromosome. chromFa.tar.gz - The assembly sequence in one file per 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. chromFaMasked.tar.gz - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.tar.gz - RepeatMasker .out files (one file per chromosome). RepeatMasker was run with the -s (sensitive) setting. Repeat masker version: June 4 2009 (open-3-2-8) Library release 20090604 chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into UCSC's BED 5+ format (one file per chromosome). md5sum.txt - checksums of files in this directory mrna.fa.gz - Tetraodon mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. 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. tetNig2.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. tetNig2.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/tetNig2/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/tetNig2/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/tetNig2/bigZips/chromFa.tar.gz' -O chromFa.tar.gz To unpack the *.tar.gz files: tar xvzf <file>.tar.gz To uncompress the fa.gz files: gunzip <file>.fa.gz The Tetraodon sequence has been freely provided by Genoscope before publication for use in the UCSC Genome Browser with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions, provided that the Genoscope is properly acknowledged. 3. Genoscope reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a Tetraodon chromosome (that is, 5 Mb or more). 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - chromAgp.tar.gz 2010-01-06 16:29 393K chromFa.tar.gz 2010-01-06 16:30 96M chromFaMasked.tar.gz 2010-01-06 16:32 81M chromOut.tar.gz 2010-01-06 16:29 4.3M chromTrf.tar.gz 2010-01-06 16:32 1.8M genes/ 2020-10-02 13:39 - md5sum.txt 2010-05-20 16:08 301 mrna.fa.gz 2020-02-27 15:15 30M mrna.fa.gz.md5 2020-02-27 15:15 45 tetNig2.2bit 2009-08-07 12:27 98M tetNig2.chrom.sizes 2009-08-06 10:29 415 tetNig2.chromAlias.txt 2020-09-29 10:49 340 tetNig2.fa.gz 2020-01-23 02:26 96M upstream1000.fa.gz 2020-02-27 15:26 769K upstream1000.fa.gz.md5 2020-02-27 15:26 53 upstream2000.fa.gz 2020-02-27 15:26 1.4M upstream2000.fa.gz.md5 2020-02-27 15:26 53 upstream5000.fa.gz 2020-02-27 15:26 3.4M upstream5000.fa.gz.md5 2020-02-27 15:26 53 xenoMrna.fa.gz 2020-02-27 15:25 6.8G xenoMrna.fa.gz.md5 2020-02-27 15:26 49 xenoRefMrna.fa.gz 2020-02-27 15:26 337M xenoRefMrna.fa.gz.md5 2020-02-27 15:26 52