This directory contains the JGI v4.1 assembly of the Xenopus tropicalis genome (xenTro2, Aug. 2005) from the DOE Joint Genome Institute (JGI). Files included in this directory: xenTro2.2bit - contains the complete X. tropicalis/xenTro2 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 xenTro2.fa.gz - scaffold FASTA, with repetitive sequences identified by RepeatMasker and TRF (maxPeriod=12) masked to lower case. xenTro2.hardmasked.fa.gz - scaffold FASTA, with repetitive sequences masked to N. xenTro2.rmsk.out.gz - RepeatMasker output combined from two runs: one run with the default -species "xenopus tropicalis" libraries for version open-3-1-5 (March 20, 2006, lib releast 20060315), and another run with ftp://ftp.jgi-psf.org/pub/JGI_data/Frog/v3.0/repeats_lib/xt3.lib1.fasta.gz as the library (-lib instead of -species). xenTro2.trf.bed.gz - TRF (Tandem Repeats Finder) output, translated to UCSC's BED format. The simple repeats in this file have not been filtered to retain only maxPeriod=12 -- a maxPeriod=12 subset was extracted from this set to use in our masking. md5sum.txt - MD5 checksum of these files to verify correct transmission. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for MGC Genes with annotated 5' UTRs. This file is updated weekly so it could be slightly out of sync with the MGC Gene 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. xenTro2.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/xenTro2/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) 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 (firstname.lastname@example.org), JGI. We welcome a coordinated approach to describing this community resource. 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - xenTro2.2bit 2006-04-17 17:06 372M xenTro2.chrom.sizes 2006-04-17 17:14 383K xenTro2.fa.gz 2006-04-17 17:38 414M xenTro2.rmsk.out.gz 2006-04-17 17:41 54M xenTro2.trf.bed.gz 2006-04-17 17:41 15M xenTro2.hardmasked.fa.gz 2006-04-17 17:42 333M md5sum.txt 2013-12-10 14:04 261 mrna.fa.gz 2020-03-02 16:46 14M mrna.fa.gz.md5 2020-03-02 16:46 45 est.fa.gz 2020-03-02 16:51 306M est.fa.gz.md5 2020-03-02 16:51 44 xenoRefMrna.fa.gz 2020-03-02 16:52 330M xenoRefMrna.fa.gz.md5 2020-03-02 16:52 52 refMrna.fa.gz 2020-03-02 16:52 6.9M refMrna.fa.gz.md5 2020-03-02 16:52 48 upstream1000.fa.gz 2020-03-02 16:52 2.3M upstream1000.fa.gz.md5 2020-03-02 16:52 53 upstream2000.fa.gz 2020-03-02 16:52 4.3M upstream2000.fa.gz.md5 2020-03-02 16:52 53 upstream5000.fa.gz 2020-03-02 16:52 10M upstream5000.fa.gz.md5 2020-03-02 16:52 53