A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of
Master’s in Information and Communication Science and Engineering of the Nelson
Mandela African Institution of Science and Technology
The Sanger sequencing technique still remains the cornerstone methods for the
Deoxyribonucleic acid (DNA) sequencing. This is due to its high accuracy in targeting smaller
genomic regions in a large number of samples, sequencing of variable regions and validating
results of other DNA sequencing platforms such as those from next-generation sequencing
studies. The analysis of Sanger sequence DNA data is computationally intensive requiring
efficient and high computational power software tools. The most preferred tools are the
proprietary licensed tools since they offer user-friendly interface and they offer more DNA
analysis functionalities. However, the affordability of the tools may be limited especially for
individual researchers or students due to their expensive licenses. Nevertheless, free and open source licensed tools are available and but are not user-friendly, have steep learning curve since
some lack graphical user interface, operating system platform dependent and have limited
functionalities. This study presents a Sanger Sequence Automatic Analysis Tool (SSAAT), a
software tool designed and implemented as a web application that provides a user-friendly
graphical interface such as those provided in proprietary tools. The tool has abilities to extract
raw data from sequence AB1 files, make base-calls, plot chromatogram, polymorphism
detection, sequence alignment and report generation. Furthermore, the tool is free and open source that can be easily accessed online through standard web browser applications. With the
above-mentioned features, SSAAT can be used by molecular biologist as an alternative to
proprietary tools and get comparable experience and DNA sequence analysis results