This directory contains the Feb. 2007 assembly of the P. pacificus genome (priPac1, Washington University School of Medicine GSC Pristionchus pacificus 5.0), 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. For more information on the P. pacificus genome, see the project website: http://genome.wustl.edu/genome.cgi?GENOME=Pristionchus+pacificus+var.+california Files included in this directory: priPac1.2bit - contains the complete P. pacificus/priPac1 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. October 6 2006 (open-3-1-6) version of RepeatMasker RepBase RELEASE 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 - P. pacificus 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 - P. pacificus 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. priPac1.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/priPac1/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The P. pacificus sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing these data if the providers of these data are properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html for credit information. 3. See also: http://genome.wustl.edu/data.cgi 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - chromAgp.tar.gz 2007-05-01 10:32 521K chromFa.tar.gz 2007-05-01 10:33 45M chromFaMasked.tar.gz 2007-05-01 10:33 44M chromOut.tar.gz 2007-05-01 10:32 1.1M chromTrf.tar.gz 2007-05-01 10:33 171K est.fa.gz 2019-10-16 14:49 6.1M est.fa.gz.md5 2019-10-16 14:49 44 md5sum.txt 2014-01-03 15:58 301 mrna.fa.gz 2019-10-16 14:44 43K mrna.fa.gz.md5 2019-10-16 14:44 45 priPac1.2bit 2007-03-04 21:36 42M priPac1.chrom.sizes 2007-03-04 20:24 16 priPac1.fa.gz 2020-01-23 02:25 45M xenoMrna.fa.gz 2016-03-21 12:14 5.0G xenoMrna.fa.gz.md5 2016-03-21 12:14 49 xenoRefMrna.fa.gz 2019-10-16 14:49 331M xenoRefMrna.fa.gz.md5 2019-10-16 14:49 52