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.
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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 (pmrichardson@lbl.gov), 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 -
xenTro1.chrom.sizes 2004-10-21 09:27 527K
xenTro1.2bit 2004-10-22 11:51 400M
repeats.zip 2004-11-05 14:52 30M
softmask2.zip 2004-11-05 14:56 419M
trf.zip 2004-11-05 15:13 15M
hardmask2.zip 2004-11-05 15:19 352M
RmLib.zip 2004-11-05 15:38 147K
xenoMrna.zip 2004-11-05 15:44 334M
scaffolds.zip 2004-11-05 15:49 393M
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
est.fa.gz 2019-10-17 23:13 306M
est.fa.gz.md5 2019-10-17 23:13 44
xenoRefMrna.fa.gz 2019-10-17 23:13 324M
xenoRefMrna.fa.gz.md5 2019-10-17 23:13 52
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.fa.gz 2020-01-23 02:26 419M