This directory contains the Mar. 2008 assembly of the C. japonica genome (UCSC version caeJap1, WUSTL School of Medicine GSC version 3.0.2) as well as repeat annotations and GenBank sequences. This assembly was produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis (WUSTL). For more information on the C. remanei genome, see the project website: http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+japonica. Files included in this directory: caeJap1.2bit - contains the complete C. japonica/caeJap1 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 WindowMasker 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. Repeat masker version: Revision 1.213 2008/01/12 01:21:36 Repeat Libraries version: RELEASE 20071204 NOTE: the WindowMasker repeat annotations were used to make the masked sequence chromWMSdust.bed.gz - bed file for chrUn used as repeat areas identified by WindowMasker with the -sdust option. 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. japonica 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. japonica 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. caeJap1.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/caeJap1/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/caeJap1/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/caeJap1/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. japonica 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 - caeJap1.2bit 2008-04-03 22:58 44M caeJap1.chrom.sizes 2008-04-03 13:48 16 caeJap1.fa.gz 2020-01-23 02:20 42M chromAgp.tar.gz 2008-06-20 14:55 901K chromFa.tar.gz 2008-06-20 14:55 42M chromFaMasked.tar.gz 2008-06-20 14:56 27M chromOut.tar.gz 2008-06-20 14:55 1.3M chromTrf.tar.gz 2008-06-20 14:56 278K est.fa.gz 2020-09-09 18:57 6.0M est.fa.gz.md5 2020-09-09 18:57 44 md5sum.txt 2013-12-12 08:54 355 mrna.fa.gz 2020-09-09 18:42 5.4K mrna.fa.gz.md5 2020-09-09 18:42 45 refMrna.fa.gz 2020-09-09 18:58 20 refMrna.fa.gz.md5 2020-09-09 18:58 48 xenoMrna.fa.gz 2020-09-09 18:53 7.0G xenoMrna.fa.gz.md5 2020-09-09 18:53 49 xenoRefMrna.fa.gz 2020-09-09 18:58 344M xenoRefMrna.fa.gz.md5 2020-09-09 18:58 52