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Automated bioinformatic discovery: tools that tell you what you should knowa case-study in synthetic biology
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Authors
Advisor(s)
Abstract(s)
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.
Description
Dissertação mest., Engenharia Biológica, Universidade do Algarve, 2009
Keywords
Teses Biologia sintética Engenharia biológica Bioinformática Python