This directory contains the Oct. 2004 assembly of the fugu genome (fr2, JGI V4.0), as well as repeat annotations and GenBank sequences. This assembly was produced by the US DOE Joint Genome Institute (JGI). For more information on the fugu genome, see the project website: http://genome.jgi-psf.org/Takru4/Takru4.info.html http://www.fugu-sg.org/ Files included in this directory: fr2.2bit - contains the complete fugu/fr2 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 chromAgp.tar.gz - Description of how the assembly was generated from scaffolds, unpacking to one file per chromosome, chrUn and chrM. chromFa.tar.gz - The assembly sequence in one file per chromosome. Repeats from WindowMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. Note, this sequence is *not* masked with the RepeatMasker .out specification. chromFaMasked.tar.gz - The assembly sequence in one file per chromosome. Gaps and 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. RepeatMasker version: October 6, 2006 (open-3-1-6) with RepBase libraries: RepBase Update 20061006. 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 format (one file per chromosome). chromWMSdust.bed.tar.gz - per-chrom bed files used as repeat areas identified by WindowMasker with the -sdust option. est.fa.gz - Fugu ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - checksums of files in this directory mrna.fa.gz - Fugu 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. fr2.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. fr2.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, then go to the directory goldenPath/fr2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) 1. These data have been freely provided by the JGI for use in the UCSC Genome Browser.
Name Last modified Size Description
Parent Directory - chromAgp.tar.gz 2007-02-14 11:23 162K chromFa.tar.gz 2007-02-14 11:24 113M chromFaMasked.tar.gz 2007-02-14 11:26 95M chromOut.tar.gz 2007-03-20 14:13 5.5M chromTrf.tar.gz 2007-02-14 11:26 1.5M chromWMSdust.bed.tar.gz 2007-02-14 11:10 11M est.fa.gz 2020-02-28 02:15 38M est.fa.gz.md5 2020-02-28 02:15 44 fr2.2bit 2007-01-23 10:30 109M fr2.chrom.sizes 2007-01-22 12:22 27 fr2.chromAlias.txt 2020-09-29 10:48 54 fr2.fa.gz 2020-01-23 02:21 113M genes/ 2020-02-05 13:47 - md5sum.txt 2014-01-03 16:13 449 mrna.fa.gz 2020-02-28 02:00 385K mrna.fa.gz.md5 2020-02-28 02:00 45 upstream1000.fa.gz 2020-02-28 02:15 112K upstream1000.fa.gz.md5 2020-02-28 02:15 53 upstream2000.fa.gz 2020-02-28 02:15 213K upstream2000.fa.gz.md5 2020-02-28 02:15 53 upstream5000.fa.gz 2020-02-28 02:15 505K upstream5000.fa.gz.md5 2020-02-28 02:15 53 xenoMrna.fa.gz 2020-02-28 02:10 6.8G xenoMrna.fa.gz.md5 2020-02-28 02:10 49