The Usability Testing of SSAAT, a Bioinformatic Web Application for DNA Analysis at a Nucleotide Level

  • V. Mero School of Computational and Communication Science and Engineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Tanzania
  • D. Machuve Nelson Mandela African Institute of Science and Technology, Tanzania

Abstract

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.

Keywords: Sanger sequence, usability, bioinformatics, web tool

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References

J. Shendure et al., "DNA sequencing at 40: past, present and future," Nature, vol. 550, no. 7676, pp. 345–353, Oct. 2017.

B. Ewing, L. Hillier, M. C. Wendl, and P. Green, "Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment," Genome Research, vol. 8, no. 3, pp. 175–185, Mar. 1998.

https://commons.wikimedia.org/wiki/File:Sanger-sequencing.svg

"Applied Biosystems Genetic Analysis Data File Format." Applied Biosystems, Jul. 2006.

B. Ewing and P. Green, "Base-calling of automated sequencer traces using phred. II. Error probabilities," Genome Research, vol. 8, no. 3, pp. 186–194, Mar. 1998.

M. Machado et al., "Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies," Investigative Genetics, vol. 2, no. 1, Feb. 2011, Art. no. 3.

B. J. Stucky, "SeqTrace: A Graphical Tool for Rapidly Processing DNA Sequencing Chromatograms," Journal of Biomolecular Techniques : JBT, vol. 23, no. 3, pp. 90–93, Sep. 2012.

T. Rausch, M. H.-Y. Fritz, A. Untergasser, and V. Benes, "Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files," BMC Genomics, vol. 21, no. 1, Mar. 2020, Art. no. 230.

J. T. Hill and B. Demarest, sangerseqR: Tools for Sanger Sequencing Data in R. Bioconductor version: Release (3.12), 2021.

A. Singh and P. Bhatia, "Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User Interference," Journal of Biomolecular Techniques : JBT, vol. 27, no. 4, pp. 129–131, Dec. 2016.

C.-T. Chang et al., "Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling," The Scientific World Journal, vol. 2012, Jun. 2012, Art. no. e365104.

D. A. Dmitriev and R. A. Rakitov, "Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels," PLOS Computational Biology, vol. 4, no. 7, 2008, Art. no. e1000113.

I. Zhidkov, R. Cohen, N. Geifman, D. Mishmar, and E. Rubin, "CHILD: a new tool for detecting low-abundance insertions and deletions in standard sequence traces," Nucleic Acids Research, vol. 39, no. 7, Apr. 2011, Art. no. e47.

M. Shitkova, J. Holler, T. Heide, N. Clever, and J. Becker, "Towards Usability Guidelines for Mobile Websites and Applications," in Wirtschaftsinformatik Proceedings, Mar. 2015.

P. T. Koziokas, N. D. Tselikas, and G. S. Tselikis, "Usability Testing of Mobile Applications: Web vs. Hybrid Apps," in Proceedings of the 21st Pan-Hellenic Conference on Informatics, New York, NY, USA, Sep. 2017, Art. no. 55.

J. R. Bergstrom and A. Schall, Eds., Eye Tracking in User Experience Design, 1st ed. Amsterdam , Netherlands; Boston, MA, USA: Morgan Kaufmann, 2014.

E. Folmer and J. Bosch, "Architecting for usability: a survey," Journal of Systems and Software, vol. 70, no. 1, pp. 61–78, Feb. 2004.

A. Fernandez, E. Insfran, and S. Abrahão, "Usability evaluation methods for the web: A systematic mapping study," Information and Software Technology, vol. 53, no. 8, pp. 789–817, Aug. 2011.

J. Nielsen, "Usability for the MassesJUS," Journal of Usability Studies, vol. 1, no. 1, pp. 2–3, Nov. 2005.

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