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The instance-based reinforcement learning methodology comes from the computer science literature, where it was developed to optimize sequences of actions in an evolving, time varying system.
This paper provides a pre-posterior analysis framework to (1) optimize sequences of actions minimizing the expected costs and satisfying reliability constraints and (2) quantify the potential gain of making measurements in existing structures.
Burke and Willis [ 76] got motivated from works of Joyce and colleagues who were the first to use point mutations through error-prone amplification and thus to optimize sequences for particular functions [ 77– 81].
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" - " was introduced to optimize sequence alignments.
Steps to optimize sequencing can also include alternative primers or denaturation conditions.
Three titration runs (each of 1/16 lane) were performed to optimize sequencing conditions.
To optimize sequencing efficiency, libraries were titrated by emulsion PCR/bead enrichment, performed as suggested by Roche 454.
Finally, if high-resolution structures are available, one can use structure-based alignments, which do not optimize sequence similarity and hence avoid sequence alignment bias altogether.
The first intron of S7 gene were aligned with Clustal X [ 138], using default parameters, to optimize sequence alignment including gaps and aligned sequences were later checked by eye.
Hence, based on the promising in silico validation results which implicate CC as an important design parameter for optimizing sequences, the newly developed CCO procedure can potentially supersede the ICU optimization techniques currently implemented in gene design software tools.
Then, the codon optimized sequences were transformed and expressed in E. coli.
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