This directory contains the Oct. 2011 (FUGU5/fr3) assembly of the fugu genome
(fr3, Fugu Genome Sequencing Consortium - FUGU5
(NCBI project 1434, GCA_000180615.2)),
as well as repeat annotations and GenBank sequences.
This assembly was produced by the Fugu Genome Sequencing Consortium,
http://www.fugu-sg.org/
as part of the International Fugu Genome Consortium, led by JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).
For more information on the fugu genome, see the project website:
http://www.fugu-sg.org/
Files included in this directory:
fr3.2bit - contains the complete fugu/fr3 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
fr3.agp.gz - Description of how the assembly was generated from
fragments.
fr3.fa.gz - "Soft-masked" 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.
fr3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
fr3.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RepeatMasker version: April 26 2011 (open-3-3-0)
with library version: RELEASE 20110920
fr3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format.
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.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts of RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it might be slightly out of sync with
the RefSeq 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.
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.
fr3.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
fr3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
fr3.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
fr3.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
fr3.chromAlias.txt - sequence name alias file, one line
for each sequence name. First column is sequence name followed by
tab separated alias names.
------------------------------------------------------------------
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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/fr3/bigZips. To download multiple files, use
the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/bigZips/chromFa.tar.gz'
-O chromFa.tar.gz
To unpack the *.tar.gz files:
tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
==============================================================================
1. These data have been freely provided by the JGI for use in the
UCSC Genome Browser.
==============================================================================
Name Last modified Size Description
Parent Directory -
genes/ 2020-02-05 13:47 -
est.fa.gz.md5 2019-10-15 19:10 44
mrna.fa.gz.md5 2019-10-15 18:55 45
refMrna.fa.gz.md5 2019-10-15 19:11 48
xenoMrna.fa.gz.md5 2019-10-15 19:06 49
upstream1000.fa.gz.md5 2019-10-15 19:11 53
upstream2000.fa.gz.md5 2019-10-15 19:11 53
upstream5000.fa.gz.md5 2019-10-15 19:11 53
md5sum.txt 2019-01-17 15:54 602
fr3.chrom.sizes 2011-11-16 11:29 95K
refMrna.fa.gz 2019-10-15 19:11 282K
fr3.chromAlias.txt 2022-09-08 14:12 307K
mrna.fa.gz 2019-10-15 18:55 385K
fr3.agp.gz 2012-02-23 15:16 417K
fr3.gc5Base.wig.gz 2019-01-17 14:47 1.5M
fr3.trf.bed.gz 2012-02-23 15:16 1.5M
fr3.chromAlias.bb 2022-09-08 14:12 1.6M
upstream1000.fa.gz 2019-10-15 19:11 2.8M
upstream2000.fa.gz 2019-10-15 19:11 5.2M
fr3.fa.out.gz 2012-02-23 15:16 5.5M
upstream5000.fa.gz 2019-10-15 19:11 12M
est.fa.gz 2019-10-15 19:10 38M
fr3.gc5Base.wib 2019-01-17 14:47 69M
fr3.fa.masked.gz 2012-02-23 15:19 94M
fr3.2bit 2011-11-17 11:51 107M
fr3.fa.gz 2012-02-23 15:18 112M
fr3.gc5Base.wigVarStep.gz 2011-11-16 11:31 174M
xenoMrna.fa.gz 2019-10-15 19:05 6.8G