This directory contains the Feb. 2004 freeze of the Tetraodon nigroviridis version 7 (V7) genome assembly (tetNig1) provided by Genoscope (http://www.genoscope.cns.fr/). This assembly is the result of a collaboration between Genoscope and the Broad Institute of MIT and Harvard in Cambridge, MA. Files included in this directory: tetNig1.2bit - contains the complete tetraodon/tetNig1 genome sequence in the 2bit file format. While we are providing the .2bit for this assembly, we will continue to use the .nib files in the Genome Browser. 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.zip - Description of how the assembly was generated, unpacking to one file per chromosome. chromFa.zip - 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. The main assembly is found in the chrN.fa files, where N is the name of the chromosome. The chrN_random.fa files contain clones that are not yet finished or cannot be placed with certainty at a specific place on the chromosome. In some cases, including the human HLA region on chromosome 6, the chrN_random.fa files also contain haplotypes that differ from the main assembly. chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period of less than or equal to 12, and translated into one .bed file per chromosome. est.fa.gz - Tetraodon ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - Checksums for each of the *.zip files. 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. tetNig1.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 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/tetNig1/bigZips/. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely usable for any purpose. 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.zip 2004-09-08 08:31 583K chromFa.zip 2004-09-08 08:34 95M chromFaMasked.zip 2004-09-08 08:37 92M chromOut.zip 2004-09-08 08:31 4.5M chromTrf.zip 2004-09-08 08:37 1.8M est.fa.gz 2012-01-03 06:44 20 est.fa.gz.md5 2012-01-03 06:44 44 md5sum.txt 2014-05-05 15:31 418 mrna.fa.gz 2019-10-17 22:30 30M mrna.fa.gz.md5 2019-10-17 22:30 45 tetNig1.2bit 2004-08-17 21:10 98M tetNig1.chrom.sizes 2004-08-17 20:26 422 tetNig1.fa.gz 2020-01-23 02:26 95M upstream1000.fa.gz 2019-10-17 22:30 1.4M upstream1000.fa.gz.md5 2019-10-17 22:30 53 upstream2000.fa.gz 2019-10-17 22:30 2.7M upstream2000.fa.gz.md5 2019-10-17 22:30 53 upstream5000.fa.gz 2019-10-17 22:30 6.4M upstream5000.fa.gz.md5 2019-10-17 22:30 53 xenoMrna.fa.gz 2016-02-27 18:41 4.9G xenoMrna.fa.gz.md5 2016-02-27 18:41 49 xenoMrna.zip 2005-01-09 23:10 320M xenoRefMrna.fa.gz 2019-10-17 22:30 331M xenoRefMrna.fa.gz.md5 2019-10-17 22:30 52