This directory contains the Mar. 2008 assembly of the C. japonica genome
(UCSC version caeJap1, WUSTL School of Medicine GSC version 3.0.2)
as well as repeat annotations and GenBank sequences.
This assembly was produced by the Genome Sequencing Center at
the Washington University School of Medicine in St. Louis (WUSTL).
For more information on the C. remanei genome, see the project website:
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+japonica.
Files included in this directory:
caeJap1.2bit - contains the complete C. japonica/caeJap1 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
fragments, unpacking to one file per chromosome.
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.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
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.
Repeat masker version: Revision 1.213 2008/01/12 01:21:36
Repeat Libraries version: RELEASE 20071204
NOTE: the WindowMasker repeat annotations were used to make the
masked sequence
chromWMSdust.bed.gz - bed file for chrUn used as repeat areas
identified by WindowMasker with the -sdust option.
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).
est.fa.gz - C. japonica 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 - C. japonica 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.
caeJap1.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 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/caeJap1/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/caeJap1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/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
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The C. japonica sequence is made freely available to the community by the
Genome Sequencing Center at the WUSTL School of Medicine. Please see the
WUSTL data use policy at http://genome.wustl.edu/data.cgi for data use
restrictions and citation information.
Name Last modified Size Description
Parent Directory -
caeJap1.2bit 2008-04-03 22:58 44M
caeJap1.chrom.sizes 2008-04-03 13:48 16
caeJap1.fa.gz 2020-01-23 02:20 42M
chromAgp.tar.gz 2008-06-20 14:55 901K
chromFa.tar.gz 2008-06-20 14:55 42M
chromFaMasked.tar.gz 2008-06-20 14:56 27M
chromOut.tar.gz 2008-06-20 14:55 1.3M
chromTrf.tar.gz 2008-06-20 14:56 278K
est.fa.gz 2019-10-14 21:48 6.0M
est.fa.gz.md5 2019-10-14 21:48 44
md5sum.txt 2013-12-12 08:54 355
mrna.fa.gz 2019-10-14 21:35 5.4K
mrna.fa.gz.md5 2019-10-14 21:35 45
refMrna.fa.gz 2019-10-14 21:49 20
refMrna.fa.gz.md5 2019-10-14 21:49 48
xenoMrna.fa.gz 2019-10-14 21:44 6.8G
xenoMrna.fa.gz.md5 2019-10-14 21:44 49
xenoRefMrna.fa.gz 2019-10-14 21:49 331M
xenoRefMrna.fa.gz.md5 2019-10-14 21:49 52