The Usability Testing of SSAAT, a Bioinformatic Web Application for DNA Analysis at a Nucleotide Level
Received: 21 February 2021 | Revised: 28 March 2021 | Accepted: 3 April 2021 | Online: 12 June 2021
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
J. Shendure et al., "DNA sequencing at 40: past, present and future," Nature, vol. 550, no. 7676, pp. 345–353, Oct. 2017. DOI: https://doi.org/10.1038/nature24286
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. DOI: https://doi.org/10.1101/gr.8.3.175
"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. DOI: https://doi.org/10.1101/gr.8.3.186
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. DOI: https://doi.org/10.1186/2041-2223-2-3
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. DOI: https://doi.org/10.7171/jbt.12-2303-004
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. DOI: https://doi.org/10.1186/s12864-020-6635-8
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. DOI: https://doi.org/10.7171/jbt.16-2704-005
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. DOI: https://doi.org/10.1100/2012/365104
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. DOI: https://doi.org/10.1371/journal.pcbi.1000113
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. DOI: https://doi.org/10.1093/nar/gkq1354
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. DOI: https://doi.org/10.1145/3139367.3139410
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. DOI: https://doi.org/10.1016/S0164-1212(02)00159-0
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. DOI: https://doi.org/10.1016/j.infsof.2011.02.007
J. Nielsen, "Usability for the MassesJUS," Journal of Usability Studies, vol. 1, no. 1, pp. 2–3, Nov. 2005.
How to Cite
MetricsAbstract Views: 359
PDF Downloads: 318
Copyright (c) 2021 Authors
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain the copyright and grant the journal the right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) after its publication in ETASR with an acknowledgement of its initial publication in this journal.