This directory contains the Oct. 2004 assembly of the Xenopus tropicalis genome (xenTro1, Oct. 2004) from the DOE Joint Genome Institute (JGI). Files included in this directory: xenTro1.2bit - contains the complete X. tropicalis/xenTro1 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 RmLib.zip - The RepeatMasker library file, xt3.lib1.fasta, downloaded from JGI, 10/15/04. est.fa.gz - X. tropicalis ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. hardmask2.zip - The hard masked file. The assembly sequence in one file. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. md5sum.txt - MD5 checksum of these files to verify correct transmission. mrna.fa.gz - X. tropicalis mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. repeats.zip - RepeatMasker .out file for scaffolds. These were created by RepeatMasker at the -s sensitive setting. scaffolds.zip - The assembly sequence file that contains all scaffolds in one file, xenopus.041015.fasta, downloaded from JGI, 10/15/04. softmask2.zip - The soft Masked file. The 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. trf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file. 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. xenTro1.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/xenTro1/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 - RmLib.zip 2004-11-05 15:38 147K est.fa.gz 2019-10-17 23:13 306M est.fa.gz.md5 2019-10-17 23:13 44 hardmask2.zip 2004-11-05 15:19 352M md5sum.txt 2014-02-03 10:25 455 mrna.fa.gz 2019-10-17 23:08 14M mrna.fa.gz.md5 2019-10-17 23:08 45 repeats.zip 2004-11-05 14:52 30M scaffolds.zip 2004-11-05 15:49 393M softmask2.zip 2004-11-05 14:56 419M trf.zip 2004-11-05 15:13 15M upstream1000.fa.gz 2019-10-17 23:14 2.3M upstream1000.fa.gz.md5 2019-10-17 23:14 53 upstream2000.fa.gz 2019-10-17 23:14 4.3M upstream2000.fa.gz.md5 2019-10-17 23:14 53 upstream5000.fa.gz 2019-10-17 23:14 10M upstream5000.fa.gz.md5 2019-10-17 23:14 53 xenTro1.2bit 2004-10-22 11:51 400M xenTro1.chrom.sizes 2004-10-21 09:27 527K xenTro1.fa.gz 2020-01-23 02:26 419M xenoMrna.zip 2004-11-05 15:44 334M xenoRefMrna.fa.gz 2019-10-17 23:13 324M xenoRefMrna.fa.gz.md5 2019-10-17 23:13 52