Summary
This paper presents ISAS (Interactive Software for Assisting Shuffling Process), software that has been designed and developed by the authors as a tool for assisting users conducting DNA shuffling experiments in laboratories. ISAS can be defined as a new friendly dialog box-based environment which provides many different functions for DNA analyses, including (a) the evaluation of the adequacy of parental sequences as candidates for undergoing shuffling processes and (b) the evaluation of the vast amount of sequences produced by a shuffling process in order to identify those that might be improved versions of the parental sequences. In order to exemplify some of ISAS's functionalities, the paper describes its use in assisting a laboratory shuffling experiment using two genes encoding cystatins as parental sequences, one from sugarcane and the other from rice.
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Isas: Interactive Software for Assisting Shuffling Process
1. Introduction
Directed molecular evolution is a strategy for improving a specific biological function through genetic diversification and selection, mimicking natural evolution, but in a guided and accelerated fashion [I]. The starting point of directed molecular evolution is a library of molecules and its basic strategy is recombination, a cyclic process that seeks to assemble new functional sequences from the previous sequences.A library built by using a mutagenesis process from one or a few molecules known to have a desired property is more effective than building a library using random molecules. A few similar molecules have a better chance of recombination while keeping diversity under control. The production of molecular diversity through mutagenesis is of fundamental importance in all directed evolution protocols.Many techniques for mutagenesis, such as DNA shuffling [2], [3], heteroduplex recombination [4], staggered extension (StEP, [5]), error-prone PCR [6], and a few others [7] have been developed. The DNA shuffling technique, which has been widely used for optimizing complex properties contained within DNA and proteins [8] , [9] , [10] , [11] is of particular interest in this paper.The remainder of this paper is organized as follows: Section 2 presents a brief description of the main characteristics of a DNA shuffling process, Section 3 presents the ...See the full content of this document
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