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:
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
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
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
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
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.
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