This directory contains a dump of the UCSC genome annotation database for the Nov. 2009 (JGI 4.2/xenTro3) assembly of the Xenopus (Silurana) tropicalis (western clawed frog) genome (xenTro3, US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1)) from the X. tropicalis Genome Consortium. The annotations were generated by UCSC and collaborators worldwide. This assembly was produced by the US DOE Joint Genome Institute (JGI). For more information on the X. tropicalis genome, please note the NCBI WGS Traces information: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC01 and the project website: http://genome.jgi-psf.org/Xentr4/Xentr4.home.html Files included in this directory: xenTro3.2bit - contains the complete X. tropicalis/xenTro3 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 xenTro3.agp.gz - Description of how the assembly was generated from fragments. xenTro3.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. xenTro3.fa.masked.gz - "Hard-masked" assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. xenTro3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting. RepeatMasker version: June 30 2010 (open-3-2-9) library version RELEASE 20090604 xenTro3.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 - X. tropicalis 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 - X. tropicalis 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. xenTro3.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. xenTro3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used - to construct the GC Percent track xenTro3.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 xenTro3.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 xenTro3.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/xenTro3/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/xenTro3/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/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 ========================================================================== Data use policy from: http://genome.jgi-psf.org/Xentr4/Xentr4.download.html Preliminary drafts of the X. tropicalis sequence are made freely available before scientific publication by the JGI and the X. tropicalis Genome Consortium, 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 if the provider of this data (DOE Joint Genome Institute) is properly acknowledged. 3. Additional shotgun sequencing is ongoing, and future assembly releases will be made in a timely fashion. We expect to publish an initial analysis of a high quality draft X. tropicalis genome sequence in 2005 (with submission targeted for the spring of 2005) which will include descriptions of the large scale organization of the frog genome as well as genome-scale comparisons of the frog sequence and gene set with those of other animals. Others who would like to coordinate other genome-wide analysis with this work should contact Paul Richardson (pmrichardson@lbl.gov), JGI. We welcome a coordinated approach to describing this community resource. 4. Any redistribution of the data should carry this notice. ==========================================================================