This directory contains v.3.0 draft assembly of the Fugu rubripes
genome (fr1, Aug. 2002) provided by the US DOE Joint Genome
Institute (JGI).
Files included in this directory:
fr1.2bit - contains the complete fugu/fr1 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.zip - Description of how the scaffolds are layed out
in the unordered "chromosome".
chromFa.zip - The draft sequence as a set of scaffolds in an unordered
"chromosome", as a single file, chrUn.fa. Repeats from
RepeatMasker and Tandem Repeats Finder (with period of 12 or less)
are in lower case while non-repeating sequence is in upper case.
chromFaMasked.zip - the draft sequence scaffolds, in a single file,
chrUn.hardmasked.fa, representing the unordered "chromosome".
Repeats are masked by capital N's; non-repeating sequence
is shown in upper case.
chromOut.zip - RepeatMasker .out file (chrUn.out), for the single unordered
"chromosome". This was created with RepeatMasker at the -s sensitive
setting.
chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, translated into one .bed file
for the unordered "chromosome".
contigFa.zip - The draft sequence scaffolds, with multiple scaffolds
per file, to avoid taxing directory limits. Repeats from
RepeatMasker and Tandem Repeats Finder (with period of 12 or less)
are in lower case while non-repeating sequence is in upper case.
contigFaMasked.zip - the draft sequence scaffolds, with multiple scaffolds
per file. Repeats are masked by capital N's and
non-repeating sequence is shown in upper case.
contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12. Multiple scaffolds are
collected into .bed files to avoid overtaxing directory limits.
est.fa.gz - Sequences of all Fugu ESTs in GenBank deposited as of
Aug. 2002.
liftAll.zip - A file that contains the offsets of scaffolds within
the unordered "chromosome" (chrUn).
md5sum.txt - Checksums of files in this directory.
mrna.zip - Fugu mRNA from GenBank.
xenoMrna.zip - All GenBank mRNA from species other than that of the genome.
fr1.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/fr1/bigZips/. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Name Last modified Size Description
Parent Directory -
fr1.chrom.sizes 2003-06-01 21:01 16
upstream1000.fa.gz 2019-10-17 04:05 20
upstream2000.fa.gz 2019-10-17 04:05 20
upstream5000.fa.gz 2019-10-17 04:05 20
est.fa.gz.md5 2019-10-17 04:05 44
mrna.fa.gz.md5 2019-10-17 04:00 45
xenoMrna.fa.gz.md5 2012-10-11 07:33 49
upstream1000.fa.gz.md5 2019-10-17 04:05 53
upstream2000.fa.gz.md5 2019-10-17 04:05 53
upstream5000.fa.gz.md5 2019-10-17 04:05 53
md5sum.txt 2014-02-03 10:24 519
liftAll.zip 2003-08-29 15:05 281K
mrna.fa.gz 2019-10-17 04:00 385K
chromAgp.zip 2003-08-29 14:45 444K
chromTrf.zip 2003-08-29 15:05 2.0M
contigTrf.zip 2003-08-29 15:05 2.3M
chromOut.zip 2003-08-29 14:45 4.4M
est.fa.gz 2019-10-17 04:05 38M
fr1.2bit 2005-11-13 16:56 85M
chromFaMasked.zip 2003-08-29 14:55 91M
contigFaMasked.zip 2003-08-29 15:05 95M
contigFa.zip 2003-08-29 15:00 97M
chromFa.zip 2003-08-29 14:50 97M
fr1.fa.gz 2020-01-23 02:21 97M
xenoMrna.fa.gz 2012-10-11 07:33 3.2G