This directory contains the Jan. 2007 assembly of the C. briggsae genome (cb3), as well as repeat annotations and GenBank sequences. This assembly was produced by Washington University in St. Louis (WUSTL) School of Medicine Genome Sequencing Center and the Sanger Institute. For more information on the C. briggsae genome, see the WUSTL project website at http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+briggsae. The sequence data may also be downloaded from: ftp://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_briggsae/assembly/Caenorhabditis_briggsae-1.0/output/chromosomes. Files included in this directory: cb3.2bit - contains the complete C. briggsae/cb3 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. The main assembly is found in the chrN.fa files, where N is the name of the chromosome. The chrN_random.fa artificial chromosome files contain clones that are not yet finished or cannot be placed with certainty at a specific place on that chromosome. The chrUn artifical chromosome contains clones that are not yet finished, and can not be oriented or assigned to any chromosome. 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: October 6, 2006 (open-3-1-6) with RepBase libraries: RepBase Update 20061006. 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. briggsae 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. briggsae 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. cb3.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, then go to the directory goldenPath/cb3/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. briggsae 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 - cb3.2bit 2007-02-25 15:37 27M cb3.chrom.sizes 2007-02-23 17:41 215 chromAgp.tar.gz 2007-04-13 14:52 15K chromFa.tar.gz 2007-04-13 15:01 32M chromFaMasked.tar.gz 2007-04-13 16:24 26M chromOut.tar.gz 2007-04-13 15:02 3.4M chromTrf.tar.gz 2007-04-13 15:02 259K est.fa.gz 2020-02-27 02:34 272K est.fa.gz.md5 2020-02-27 02:34 44 md5sum.txt 2014-01-03 15:38 297 mrna.fa.gz 2020-02-27 02:21 58K mrna.fa.gz.md5 2020-02-27 02:21 45 refMrna.fa.gz 2007-07-15 20:31 31 xenoMrna.fa.gz 2020-02-27 02:30 6.8G xenoMrna.fa.gz.md5 2020-02-27 02:30 49 xenoRefMrna.fa.gz 2020-02-27 02:35 337M xenoRefMrna.fa.gz.md5 2020-02-27 02:35 52