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>