Pathogenity islands

Charlie cckim at stanford.edu
Wed Jun 5 12:48:55 EST 2002


Carmen,

This is an interesting problem, but as far as I know it has not been
addressed computationally.  The primary problem is that "pathogenicity
islands" are not a precisely defined entity; rather, it is a somewhat
arbitrarily defined region.  I'm sure you already know some of the common
characteristics, but I will list a few for the benefit of other readers of
this post:

1) Flanked by tRNA sequences
2) %GC is low relative to the rest of the genome
3) Contain sequences that are unique to the organism
4) Often large (>20kb)

The problem is that very few of the many designated pathogenicity islands
out there actually have all of these features.  My belief is that the term
is used fairly loosely in order to spice up the data a bit.

On the other hand, it would be easy to use a combination of the above
criteria in a quick perl script.  I don't know if that's been done yet.

Tschuess,
Charlie

On 5 Jun 2002, Carmen Eckerich wrote:

> Hi all !!
>
> What is to your opinion the most suitable (online-)tool to find
> pathogenity islands in Bacteria ?!
>
> best wishes
>
> Carmen





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