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. ------------------------------------------------------------ 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 - ce2.2bit 2004-04-07 15:05 25M ce2.chrom.sizes 2004-04-13 16:58 99 ce2.fa.gz 2020-01-23 02:20 30M chromAgp.zip 2004-04-21 09:05 54K chromFa.zip 2004-04-21 09:06 30M chromFaMasked.zip 2004-04-21 09:07 26M chromOut.zip 2004-04-21 09:05 2.6M chromTrf.zip 2004-04-21 09:07 182K est.fa.gz 2020-02-27 20:44 72M est.fa.gz.md5 2020-02-27 20:44 44 md5sum.txt 2014-05-05 15:59 613 mrna.fa.gz 2020-02-27 20:40 1.7M mrna.fa.gz.md5 2020-02-27 20:40 45 refMrna.fa.gz 2020-02-27 20:45 17M refMrna.fa.gz.md5 2020-02-27 20:45 48 upstream1000.fa.gz 2020-02-27 20:45 5.4M upstream1000.fa.gz.md5 2020-02-27 20:45 53 upstream2000.fa.gz 2020-02-27 20:45 10M upstream2000.fa.gz.md5 2020-02-27 20:45 53 upstream5000.fa.gz 2020-02-27 20:46 23M upstream5000.fa.gz.md5 2020-02-27 20:46 53 xenoMrna.zip 2004-04-21 09:43 276M xenoRefMrna.fa.gz 2020-02-27 20:45 320M xenoRefMrna.fa.gz.md5 2020-02-27 20:45 52