Genotyping-by-sequencing

Fig. 1. Partitioning of the complex phenomenon of evolution into three simpler processes. Population dynamics is tantamount to population genetics of asexually reproducing haploid populations or chemical kinetics of polynucleotide replication. Population support dynamics describes the migration of populations in genotype or sequence space during the course of evolutionary optimization. Genotype-phenotype mapping deals with the unfolding of a phenotype under the conditions and constraints provided by the environment. It represents the major source of complexity in evolution.

The equation expresses that the space of all genotypes, the sequence space I, is a discrete space with the Hamming distance as metric. It is mapped onto a discrete space of structures called shape space with the structure distance as metric (We use I rather than 4 in order to indicate different numbering schemes used for sequences and structures). The evolutionarily relevant quantity, the fitness value fk as shown in Fig. 2.3, is derived from the phenotype Sk through evaluation, which can be understood as another mapping, a map from shape space into the positive real numbers including zero, fk = f(Sk). Both maps need not be invertible in the sense that more than one phenotype may have the same fitness value, and more than one sequence may lead to the same structure. We shall study here neutrality induced by the first map, (// in Eq. (6). 

CUronna, M., Lopaico, P., Prato, R., Germlnario, C., Barbnti, S., Quarto, M. Outbreak of infection with hepatitis A virus (HAV) associated with a foodhandler and confirmed by sequence analysis reveals a new HAV genotype 1 B variant. J. Chn. Microbiol. 2004 42 2825-2828... 

Bukh J, Purcell RH, Miller RH. At least 12 genotypes of hepatitis C virus pi edicted by sequence analysis of the putative El gene of isolates collected worldwide. Proc Natl Acad Sci USA 1993 90 8234-8. 

DNA Sequencing and Genotyping by Free-Solution Conjugate Electrophoresis... 

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