10.1371/journal.pone.0100400.g001 Michael Golden Michael Golden Brejnev M. Muhire Brejnev M. Muhire Yves Semegni Yves Semegni Darren P. Martin Darren P. Martin Diagrammatic representation of how simulated recombinants were generated. Public Library of Science 2014 Biochemistry proteins protein structure Nucleic acids cell biology Molecular cell biology molecular biology Molecular biology techniques Sequencing techniques Sequence analysis Macromolecular structure analysis Computational biology Genome evolution genetics genomics Structural genomics microbiology Medical microbiology Microbial pathogens Viral pathogens Immunodeficiency viruses hiv Virology Viral replication Viral nucleic acid Viral structure Infectious diseases Viral diseases simulated recombinants 2014-06-17 03:06:32 Figure https://plos.figshare.com/articles/figure/_Diagrammatic_representation_of_how_simulated_recombinants_were_generated_/1059825 <p>For a particular recombination event specifying a major parent, a minor parent, and a pair of recombination breakpoint locations delineating a fragment of sequence derived from the minor parent (containing in this particular case two nucleotides that vary between the major and minor parents), an <i>in silico</i> mimic of the real recombinant sequence is created using the minor and the major parent sequences. Following that, a set of N simulated recombinants is generated in a similar way to the mimic recombinant, but using random starting and ending positions, whilst maintaining the same number of either variable nucleotides (for the RNA folding tests) or non-synonymous codon sites (for the protein folding tests) between the randomized breakpoint sites as occur in the mimic recombinant. In this example the mimic and simulated recombinants all have two such “informative” sites between the 3′ and 5′ breakpoints that are not identical between the parental sequences.</p>