Pathogenity islands

Keith James kdj at
Thu Jun 6 04:01:00 EST 2002

>>>>> "Charlie" == Charlie  <cckim at> writes:

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

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

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

As Charlie points out, how you might try to accomplish this depends on
what you mean by a "pathogenicity island". For example, if you were
looking for such regions in enteric pathogens you might try Blasting
against a database of known "islands" or classes of genes (iron
uptake, type III/IV secretion systems, prophage) in addition to the
indicators he mentioned.

Tools which we use to help us include:

tRNAscan-SE (Todd Lowe & Sean Eddy, for identifying
those tRNAs which may flank these regions.

Artemis (Kim Rutherford, for
visualising anomalous %GC / dinucleotide frequencies + tRNAs
(identified by tRNA scan) and other genomic context.

ACT (Kim Rutherford, for
visualising whole genome comparisons (some of these types of of
regions appear to be horizontally transferred).

Artemis and ACT are Java applications which run on Unix/Linux, Mac and
Windows and can be downloaded for free from the above URLs. Hope this
is of some use.



-= Keith James - kdj at - =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK

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