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 - ce6.2bit 2008-05-30 14:50 25M ce6.chrom.sizes 2008-05-30 10:33 99 ce6.fa.gz 2020-01-23 02:20 30M chromAgp.tar.gz 2008-06-20 12:25 54K chromFa.tar.gz 2008-06-20 12:25 30M chromFaMasked.tar.gz 2008-06-20 12:26 26M chromOut.tar.gz 2008-06-20 12:25 2.6M chromTrf.tar.gz 2008-06-20 12:26 189K est.fa.gz 2020-02-27 20:21 72M est.fa.gz.md5 2020-02-27 20:21 44 genes/ 2020-02-05 13:46 - md5sum.txt 2014-01-27 15:21 297 mrna.fa.gz 2020-02-27 20:06 1.7M mrna.fa.gz.md5 2020-02-27 20:06 45 refMrna.fa.gz 2020-02-27 20:21 17M refMrna.fa.gz.md5 2020-02-27 20:21 48 upstream1000.fa.gz 2020-02-27 20:21 2.8M upstream1000.fa.gz.md5 2020-02-27 20:21 53 upstream2000.fa.gz 2020-02-27 20:21 5.4M upstream2000.fa.gz.md5 2020-02-27 20:21 53 upstream5000.fa.gz 2020-02-27 20:22 13M upstream5000.fa.gz.md5 2020-02-27 20:22 53 xenoMrna.fa.gz 2020-02-27 20:16 6.8G xenoMrna.fa.gz.md5 2020-02-27 20:16 49 xenoRefMrna.fa.gz 2020-02-27 20:21 320M xenoRefMrna.fa.gz.md5 2020-02-27 20:21 52