Mirjana Domazet-Lošo1, Bernhard Haubold. 1. Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany.
Abstract
MOTIVATION: Bacterial and viral genomes are often affected by horizontal gene transfer observable as abrupt switching in local homology. In addition to the resulting mosaic genome structure, they frequently contain regions not found in close relatives, which may play a role in virulence mechanisms. Due to this connection to medical microbiology, there are numerous methods available to detect horizontal gene transfer. However, these are usually aimed at individual genes and viral genomes rather than the much larger bacterial genomes. Here, we propose an efficient alignment-free approach to describe the mosaic structure of viral and bacterial genomes, including their unique regions. RESULTS: Our method is based on the lengths of exact matches between pairs of sequences. Long matches indicate close homology, short matches more distant homology or none at all. These exact match lengths can be looked up efficiently using an enhanced suffix array. Our program implementing this approach, alfy (ALignment-Free local homologY), efficiently and accurately detects the recombination break points in simulated DNA sequences and among recombinant HIV-1 strains. We also apply alfy to Escherichia coli genomes where we detect new evidence for the hypothesis that strains pathogenic in poultry can infect humans. AVAILABILITY: alfy is written in standard C and its source code is available under the GNU General Public License from http://guanine.evolbio.mpg.de/alfy/. The software package also includes documentation and example data.
MOTIVATION: Bacterial and viral genomes are often affected by horizontal gene transfer observable as abrupt switching in local homology. In addition to the resulting mosaic genome structure, they frequently contain regions not found in close relatives, which may play a role in virulence mechanisms. Due to this connection to medical microbiology, there are numerous methods available to detect horizontal gene transfer. However, these are usually aimed at individual genes and viral genomes rather than the much larger bacterial genomes. Here, we propose an efficient alignment-free approach to describe the mosaic structure of viral and bacterial genomes, including their unique regions. RESULTS: Our method is based on the lengths of exact matches between pairs of sequences. Long matches indicate close homology, short matches more distant homology or none at all. These exact match lengths can be looked up efficiently using an enhanced suffix array. Our program implementing this approach, alfy (ALignment-Free local homologY), efficiently and accurately detects the recombination break points in simulated DNA sequences and among recombinant HIV-1 strains. We also apply alfy to Escherichia coli genomes where we detect new evidence for the hypothesis that strains pathogenic in poultry can infect humans. AVAILABILITY: alfy is written in standard C and its source code is available under the GNU General Public License from http://guanine.evolbio.mpg.de/alfy/. The software package also includes documentation and example data.
Authors: Nicholas J Loman; Chrystala Constantinidou; Jacqueline Z M Chan; Mihail Halachev; Martin Sergeant; Charles W Penn; Esther R Robinson; Mark J Pallen Journal: Nat Rev Microbiol Date: 2012-08-06 Impact factor: 60.633