This directory contains the Oct. 2004 assembly of the fugu genome
(fr2, JGI V4.0), as well as repeat annotations and GenBank sequences.
This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the fugu genome, see the project website:
http://genome.jgi-psf.org/Takru4/Takru4.info.html
http://www.fugu-sg.org/
Files included in this directory:
fr2.2bit - contains the complete fugu/fr2 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
chromAgp.tar.gz - Description of how the assembly was generated from
scaffolds, unpacking to one file per chromosome, chrUn and chrM.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
Repeats from WindowMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case. Note, this sequence is *not* masked with
the RepeatMasker .out specification.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Gaps and Repeats are masked by capital Ns; non-repeating sequence is
shown in upper case.
chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
RepeatMasker version: October 6, 2006 (open-3-1-6)
with RepBase libraries: RepBase Update 20061006.
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format (one file per chromosome).
chromWMSdust.bed.tar.gz - per-chrom bed files used as repeat areas
identified by WindowMasker with the -sdust option.
est.fa.gz - Fugu 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 - Fugu mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
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.
fr2.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
fr2.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
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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, then
go to the directory goldenPath/fr2/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
1. These data have been freely provided by the JGI for use in the
UCSC Genome Browser.
Name Last modified Size Description
Parent Directory -
fr2.chrom.sizes 2007-01-22 12:22 27
fr2.2bit 2007-01-23 10:30 109M
chromWMSdust.bed.tar.gz 2007-02-14 11:10 11M
chromAgp.tar.gz 2007-02-14 11:23 162K
chromFa.tar.gz 2007-02-14 11:24 113M
chromFaMasked.tar.gz 2007-02-14 11:26 95M
chromTrf.tar.gz 2007-02-14 11:26 1.5M
chromOut.tar.gz 2007-03-20 14:13 5.5M
md5sum.txt 2014-01-03 16:13 449
mrna.fa.gz 2019-10-17 03:44 385K
mrna.fa.gz.md5 2019-10-17 03:44 45
xenoMrna.fa.gz 2019-10-17 03:53 6.8G
xenoMrna.fa.gz.md5 2019-10-17 03:53 49
est.fa.gz 2019-10-17 03:57 38M
est.fa.gz.md5 2019-10-17 03:57 44
upstream1000.fa.gz 2019-10-17 03:57 112K
upstream1000.fa.gz.md5 2019-10-17 03:57 53
upstream2000.fa.gz 2019-10-17 03:57 213K
upstream2000.fa.gz.md5 2019-10-17 03:57 53
upstream5000.fa.gz 2019-10-17 03:57 505K
upstream5000.fa.gz.md5 2019-10-17 03:57 53
fr2.fa.gz 2020-01-23 02:21 113M
genes/ 2020-02-05 13:47 -
fr2.chromAlias.txt 2022-09-08 14:12 23
fr2.chromAlias.bb 2022-09-08 14:12 22K