Automated bioinformatic discovery: tools that tell you what you should know A case-study in synthetic biology

Abstract

The large number of bioinformatics tools currently available for the analysis of genetic sequences and the technical features that each tool presents make the biological engineer's job simultaneously easier and more complex. The emerging field of synthetic biology is seen as a new approach to engineering biology, where foundational technologies and concepts generally applied to established fields of engineering, such as electrical or software engineering, are implemented in biology to enable the development of methodologies and standards to make engineering biology a predictable, reproducible and efficient task. Focusing on this new field of synthetic biology, the objective of this thesis was to develop a compound bioinformatics web application to assist in the conception and preparation of standardized biological parts, essential to the progress of this novel field. Different assembly standards for biological parts, developed and implemented by the community of biological engineers and researchers working in the field of synthetic biology, were analyzed and incorporated into the web application. The main programming language used for the development of this project was Python, with special usage of the biological computation code library provided by the BioPython project. Within the objective of producing a simple and unique web application, a selection of tools were integrated programmatically so as to generate a comprehensive analysis report of features based on a single input - a DNA or RNA sequence. This automated procedure made for a streamlined user interface with minimal learning requirements or user interaction. The provided results of the analysis performed by the web application are presented in the form of a report with information regarding the input sequence. These results include information such as for example, the identification of specific restriction sites, thermodynamic stability and secondary structure. These easily generated results provide biological engineers with information that may allow decisions to be made regarding the eligibility of the initial input sequence to be refined into a standard biological part, which in turn are elementary components in the development of synthetic biological devices or systems