IslandPathversion 1.0

An aid to the identification of genomics islands, including pathogenicity islands, of potentially horizontally transferred genes



This page allows you to download the IslandPath organism annotation files, the list of available organisms, as well as the IslandPath source code and documentation.

If you make use of the resources and/or the IslandPath web tools in your research, please cite:

William Hsiao, Ivan Wan, Steven J. Jones, and Fiona S.L. Brinkman (2003) IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 19(3):418-420 PMID:12584130

Organism Annotation Files:
These files contain the same information that shows up in the table below the IslandPath graphics. Instead of viewing only 100 ORFs at a time, you have the options of downloading the entire dataset. We offer the files as a single compressed tar file (tar.gz). To exapnd the file use the command "tar xvfz gctfiles.tar.gz" or use programs like WinZip.

Click HERE to download the annotation files (73.36MB).

List of available organisms and their genomic sequence composition summaries:
This is the IslandPath organism table in tab delimited format. The tar file (to expand, use the command "tar xvf organisms.tar" or use WinZip ) contains 3 lists correspond to pathogens, nonpathogens, and archaeas.

Click HERE to download the organism lists (225.28KB).

IslandPath source code and genoconv file:

IslandPath source code is no longer being maintained. To carry out IslandPath analysis, we recommend that you check out the new software developed in our lab, IslandViewer. It incorporates IslandPath and has additional functions for genomic island analysis. The IslandViewer source code can be downloaded here.

IslandIslandPath is written in Perl and Perl-CGI. It has been tested under Linux (Redhat and Suse distributions). The source code is available for download under the GNU General Public License (GNU GPL). The source code and documentation is provided as a compressed tar file.

If you still would like to get a copy of the old IslandPath source code, please contact us directly for it.

IslandPath uses a "genoconv" (genome ID conversion) file to recognize the different identifiers associated with the same organism (see IslandPath manual distributed with the source code for more information). The latest version of the genoconv file can be downloaded for local use.

Click HERE to download/view the genoconv.txt file (some browsers may require right clicking to save).


Last Updated: Dec 11, 2007

Funding for this work was provided by the Peter Wall Institute for Advanced Studies. This service is hosted by the Brinkman Laboratory of the Department of Molecular Biology and Biochemistry at Simon Fraser University.