This directory contains the May 2008 assembly of the C. elegans genome
(UCSC version ce6, WUSTL School of Medicine GSC and Sanger Institute
version WS190), as well as repeat annotations and GenBank sequences.
This assembly was produced by the Genome Sequencing Center at the
Washington University in St. Louis (WUSTL) School of Medicine and
the Sanger Institute. For more information on the
C. elegans genome, see the WUSTL project website at
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+elegans.
The sequence data may also be downloaded from:
ftp://ftp.sanger.ac.uk/pub/wormbase/WS190/CHROMOSOMES/.
Files included in this directory:
ce6.2bit - contains the complete C. elegans/ce6 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 RepeatMasker 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.
RepeatMasker version: 2008-01-12
with RepBase libraries: RepBase Update 20071204.
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. elegans 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. elegans 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 for RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could 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.
sangerGene.upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription start of WormBase genes. This includes only cases
where the transcription start is annotated separately from the
coding region start. (these are from the sangerGene table)
sangerGene.upstream2000.fa.gz - Same as sangerGene.upstream1000, but 2000 bases.
sangerGene.upstream5000.fa.gz - Same as sangerGene.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.
ce6.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
------------------------------------------------------------------
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/ce6/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/ce6/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ce6/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce6/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce6/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
------------------------------------------------------------------
The C. elegans 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 -
ce6.chrom.sizes 2008-05-30 10:33 99
ce6.2bit 2008-05-30 14:50 25M
chromAgp.tar.gz 2008-06-20 12:25 54K
chromOut.tar.gz 2008-06-20 12:25 2.6M
chromFa.tar.gz 2008-06-20 12:25 30M
chromFaMasked.tar.gz 2008-06-20 12:26 26M
chromTrf.tar.gz 2008-06-20 12:26 189K
md5sum.txt 2014-01-27 15:21 297
mrna.fa.gz 2019-10-16 21:41 1.7M
mrna.fa.gz.md5 2019-10-16 21:41 45
xenoMrna.fa.gz 2019-10-16 21:51 6.8G
xenoMrna.fa.gz.md5 2019-10-16 21:52 49
est.fa.gz 2019-10-16 21:56 72M
est.fa.gz.md5 2019-10-16 21:56 44
xenoRefMrna.fa.gz 2019-10-16 21:57 314M
xenoRefMrna.fa.gz.md5 2019-10-16 21:57 52
refMrna.fa.gz 2019-10-16 21:57 17M
refMrna.fa.gz.md5 2019-10-16 21:57 48
upstream1000.fa.gz 2019-10-16 21:57 2.8M
upstream1000.fa.gz.md5 2019-10-16 21:57 53
upstream2000.fa.gz 2019-10-16 21:57 5.4M
upstream2000.fa.gz.md5 2019-10-16 21:57 53
upstream5000.fa.gz 2019-10-16 21:57 13M
upstream5000.fa.gz.md5 2019-10-16 21:57 53
ce6.fa.gz 2020-01-23 02:20 30M
genes/ 2020-02-05 13:46 -