hide
Free keywords:
horizontal gene transfer; alignment; alignment-free; genome
comparison; bacteria
Abstract:
Bacterial epidemics are often caused
by strains that have acquired their
increased virulence through horizontal
gene transfer. Due to this association
with disease, the detection of horizontal
gene transfer continues to receive
attention from microbiologists and bioinformaticians
alike. Most software for
detecting transfer events is based on
alignments of sets of genes or of entire
genomes. But despite great advances in
the design of algorithms and computer
programs, genome alignment remains
computationally challenging. We have
therefore developed an alignment-free
algorithm for rapidly detecting horizontal
gene transfer between closely related
bacterial genomes. Our implementation
of this algorithm is called alfy for
“ALignment Free local homologY” and
is freely available from http://guanine.
evolbio.mpg.de/alfy/. In this comment
we demonstrate the application of alfy
to the genomes of Staphylococcus aureus.
We also argue that—contrary to popular
belief and in spite of increasing computer
speed—algorithmic optimization is
becoming more, not less, important if
genome data continues to accumulate at
the present rate.
