This directory contains sequence for C. elegans version WS120
deposited into Wormbase as of 1 March 2004. The sequence may also
be downloaded from WormBase at
ftp://ftp.sanger.ac.uk/pub/wormbase/FROZEN_RELEASES/WS120/CHROMOSOMES/.
Files included in this directory:
ce2.2bit - contains the complete C. elegans/ce2 genome sequence
in the 2bit file format. While we are providing the .2bit for
this assembly, we will continue to use the .nib files in
the Genome Browser. 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 assembly was generated,
unpacking to one file per chromosome.
chromFa.zip - 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. The main assembly is found in the chrN.fa
files, where N is the name of the chromosome. The chrN_random.fa
files contain clones that are not yet finished or cannot be placed
with certainty at a specific place on the chromosome. In some
cases, including the human HLA region on chromosome 6, the
chrN_random.fa files also contain haplotypes that differ from the
main assembly.
chromFaMasked.zip - The assembly sequence in one file per
chromosome. Repeats are masked by capital Ns; non-repeating
sequence is shown in upper case.
chromOut.zip - RepeatMasker .out file for chromosomes. These were
created by RepeatMasker at the -s sensitive setting.
chromTrf.zip - Tandem Repeats Finder locations, filtered to keep
repeats with period of less than or equal to 12, and translated
into one .bed 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 - MD5 checksum of these files to verify correct transmission.
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.
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.
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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/ce2/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
------------------------------------------------------------------
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 -
xenoRefMrna.fa.gz 2019-10-16 22:19 314M
xenoMrna.zip 2004-04-21 09:43 276M
est.fa.gz 2019-10-16 22:19 72M
ce2.fa.gz 2020-01-23 02:20 30M
chromFa.zip 2004-04-21 09:06 30M
chromFaMasked.zip 2004-04-21 09:07 26M
ce2.2bit 2004-04-07 15:05 25M
upstream5000.fa.gz 2019-10-16 22:20 22M
refMrna.fa.gz 2019-10-16 22:19 17M
upstream2000.fa.gz 2019-10-16 22:20 9.8M
upstream1000.fa.gz 2019-10-16 22:20 5.2M
chromOut.zip 2004-04-21 09:05 2.6M
mrna.fa.gz 2019-10-16 22:14 1.7M
chromTrf.zip 2004-04-21 09:07 182K
chromAgp.zip 2004-04-21 09:05 54K
md5sum.txt 2014-05-05 15:59 613
ce2.chrom.sizes 2004-04-13 16:58 99
upstream5000.fa.gz.md5 2019-10-16 22:20 53
upstream2000.fa.gz.md5 2019-10-16 22:20 53
upstream1000.fa.gz.md5 2019-10-16 22:20 53
xenoRefMrna.fa.gz.md5 2019-10-16 22:19 52
refMrna.fa.gz.md5 2019-10-16 22:19 48
mrna.fa.gz.md5 2019-10-16 22:14 45
est.fa.gz.md5 2019-10-16 22:19 44