This directory contains the Oct. 2011 (FUGU5/fr3) assembly of the fugu genome (fr3, Fugu Genome Sequencing Consortium - FUGU5 (NCBI project 1434, GCA_000180615.2)), as well as repeat annotations and GenBank sequences. This assembly was produced by the Fugu Genome Sequencing Consortium, http://www.fugu-sg.org/ as part of the International Fugu Genome Consortium, led by JGI and the Singapore Institute of Molecular and Cell Biology (IMCB). For more information on the fugu genome, see the project website: http://www.fugu-sg.org/ Files included in this directory: fr3.2bit - contains the complete fugu/fr3 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 fr3.agp.gz - Description of how the assembly was generated from fragments. fr3.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. fr3.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. fr3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version: April 26 2011 (open-3-3-0) with library version: RELEASE 20110920 fr3.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 - 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. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts of RefSeq genes with annotated 5' UTRs. This file is updated weekly so it might be slightly out of sync with the RefSeq data which is updated daily for most assemblies. upstream2000.fa.gz - Same as upstream1000, but 2000 bases. 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. fr3.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. fr3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track fr3.gc5Base.wig.gz - wiggle database table for the GC Percent track - this is an older standard alternative to the current - bigWig format of the track, sometimes usefull for analysis fr3.gc5Base.wib - binary data to correspond with the gc5Base.wig file see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database for a discussion of how to use the wig.gz and .wib files for interaction with the GC percent data values fr3.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/fr3/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/fr3/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/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 ============================================================================== 1. These data have been freely provided by the JGI for use in the UCSC Genome Browser. ==============================================================================