Sanger sequence automatic analysis tool development

Abstract

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