Cargando…
gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances
Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of compl...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112998/ https://www.ncbi.nlm.nih.gov/pubmed/27846272 http://dx.doi.org/10.1371/journal.pone.0166602 |
_version_ | 1782468120431034368 |
---|---|
author | Domazet-Lošo, Mirjana Domazet-Lošo, Tomislav |
author_facet | Domazet-Lošo, Mirjana Domazet-Lošo, Tomislav |
author_sort | Domazet-Lošo, Mirjana |
collection | PubMed |
description | Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos). |
format | Online Article Text |
id | pubmed-5112998 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-51129982016-12-08 gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances Domazet-Lošo, Mirjana Domazet-Lošo, Tomislav PLoS One Research Article Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos). Public Library of Science 2016-11-15 /pmc/articles/PMC5112998/ /pubmed/27846272 http://dx.doi.org/10.1371/journal.pone.0166602 Text en © 2016 Domazet-Lošo, Domazet-Lošo http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Domazet-Lošo, Mirjana Domazet-Lošo, Tomislav gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances |
title | gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances |
title_full | gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances |
title_fullStr | gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances |
title_full_unstemmed | gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances |
title_short | gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances |
title_sort | gmos: rapid detection of genome mosaicism over short evolutionary distances |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112998/ https://www.ncbi.nlm.nih.gov/pubmed/27846272 http://dx.doi.org/10.1371/journal.pone.0166602 |
work_keys_str_mv | AT domazetlosomirjana gmosrapiddetectionofgenomemosaicismovershortevolutionarydistances AT domazetlosotomislav gmosrapiddetectionofgenomemosaicismovershortevolutionarydistances |