gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances

PloS One
Mirjana Domazet-Lošo, Tomislav Domazet-Lošo

Abstract

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; f...Continue Reading

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Citations

Related Concepts

Mosaicism
Computer Programs and Programming
Determination, Sequence Homology
Genome, Bacterial
Enterococcus faecium
Sequence Determinations, DNA
Computational Molecular Biology
Recombination, Interspecies
Genome
Recombination, Genetic

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