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.
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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/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 (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 -
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 2019-10-17 22:56 14M
mrna.fa.gz.md5 2019-10-17 22:56 45
est.fa.gz 2019-10-17 23:01 306M
est.fa.gz.md5 2019-10-17 23:01 44
xenoRefMrna.fa.gz 2019-10-17 23:02 324M
xenoRefMrna.fa.gz.md5 2019-10-17 23:02 52
refMrna.fa.gz 2019-10-17 23:02 6.7M
refMrna.fa.gz.md5 2019-10-17 23:02 48
upstream1000.fa.gz 2019-10-17 23:02 2.3M
upstream1000.fa.gz.md5 2019-10-17 23:02 53
upstream2000.fa.gz 2019-10-17 23:02 4.4M
upstream2000.fa.gz.md5 2019-10-17 23:02 53
upstream5000.fa.gz 2019-10-17 23:02 10M
upstream5000.fa.gz.md5 2019-10-17 23:02 53