Sequencing approaches, comparison

Comparison of Nucleic Acids from Microorganisms Sequencing Approaches... 

A general method has been developed for the estimation of model parameters from experimental observations when the model relating the parameters and input variables to the output responses is a Monte Carlo simulation. The method provides point estimates as well as joint probability regions of the parameters. In comparison to methods based on analytical models, this approach can prove to be more flexible and gives the investigator a more quantitative insight into the effects of parameter values on the model. The parameter estimation technique has been applied to three examples in polymer science, all of which concern sequence distributions in polymer chains. The first is the estimation of binary reactivity ratios for the terminal or Mayo-Lewis copolymerization model from both composition and sequence distribution data. Next a procedure for discriminating between the penultimate and the terminal copolymerization models on the basis of sequence distribution data is described. Finally, the estimation of a parameter required to model the epimerization of isotactic polystyrene is discussed. 

We have presented applications of a parameter estimation technique based on Monte Carlo simulation to problems in polymer science involving sequence distribution data. In comparison to approaches involving analytic functions, Monte Carlo simulation often leads to a simpler solution of a model particularly when the process being modelled involves a prominent stochastic coit onent. 

A further insight is that the best workflow depends on a combination of factors that can in many cases be expressed in closed mathematical form, allowing very rapid graphical feedback to users of what then becomes a visualization rather than a stochastic simulation tool. This particular approach is effective for simple binary comparisons of methods (e.g., use of in vitro alone vs. in silico as prefilter to in vitro). It can also be extended to evaluation of conditional sequencing for groups of compounds, using an extension of the sentinel approach [24]. 

Figure 2 Comparison of cloning and expression methods. In the conventional strategy (left), dehydrogenase genes obtained by PCR amplification of the original source DNAs are cloned into overexpression plasmids and verified by sequencing. Those with the desired structure are individually transformed into suitable host strains and the proteins are obtained, either as crude extracts or as purified samples. In the proposed streamlined approach (right), full-length dehydrogenase genes obtained by chemical synthesis are used directly in coupled transcription/translation reactions to obtain the proteins of interest.

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