Browsing by Author "Mero, Victor"

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    Sanger sequence automatic analysis tool development
    (NM-AIST, 2021-08) Mero, Victor
    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
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    The Usability Testing of SSAAT, a Bioinformatic Web Application for DNA Analysis at a Nucleotide Level
    (Engineering, Technology & Applied Science Research, 2021-06) Mero, Victor; Machuve, Dina
    Sanger sequencing remains the cornerstone method for Deoxyribonucleic Acid (DNA) sequencing due to its high accuracy in targeting smaller genomic regions in a larger number of samples. The analysis of Sanger sequence DNA data requires powerful and intelligent software tools. Most of the preferred tools are proprietary licensed tools that offer a user-friendly interface and have many features, however, their affordability, especially to individual scientists or students, is limited. On the other hand, a few free and open-source licensed tools are available but have limited features. This study focuses on the usability testing of the developed Sanger Sequence Automatic Analysis Tool (SSAAT), a free and open-source web tool for Sanger sequence analysis. Usability tests were conducted with potential users and the results demonstrate that the participants were able to use the tool easily and accomplish the test tasks at the given time. Moreover, the participants were excited with the easy-to-use interface and agreed that most users could use the tool with no need for technical assistance. However, the participants also identified some issues that require more development effort.