DOI QR코드

DOI QR Code

A Python-based educational software tool for visualizing bioinformatics alignment algorithms

  • Elis Khatizah (Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University) ;
  • Hee-Jo Nam (Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University) ;
  • Hyun-Seok Park (Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University)
  • Received : 2022.08.29
  • Accepted : 2023.01.14
  • Published : 2023.03.31

Abstract

Bioinformatics education can be defined as the teaching and learning of how to use software tools, along with mathematical and statistical analysis, to solve biological problems. Although many resources are available, most students still struggle to understand even the simplest sequence alignment algorithms. Applying visualizations to these topics benefits both lecturers and students. Unfortunately, educational software for visualizing step-by-step processes in the user experience of sequence alignment algorithms is rare. In this article, an educational visualization tool for biological sequence alignment is presented, and the source code is released in order to encourage the collaborative power of open-source software, with the expectation of further contributions from the community in the future. Two different modules are integrated to enable a student to investigate the characteristics of alignment algorithms.

Keywords

References

  1. Magana AJ, Taleyarkhan M, Alvarado DR, Kane M, Springer J, Clase K. A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research. CBE Life Sci Educ 2014;13:607-623. https://doi.org/10.1187/cbe.13-10-0193
  2. Oliver J, Pisano ME, Alonso T, Roca P. The Web as an educational tool for/in learning/teaching bioinformatics statistics. Med Inform Internet Med 2005;30:255-266. https://doi.org/10.1080/14639230500367456
  3. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012;28:1647-1649. https://doi.org/10.1093/bioinformatics/bts199
  4. Hernandez-de-Diego R, de Villiers EP, Klingstrom T, Gourle H, Conesa A, Bongcam-Rudloff E. The eBioKit, a stand-alone educational platform for bioinformatics. PLoS Comput Biol 2017; 13:e1005616.
  5. Jackman SD, Mozgacheva T, Chen S, O'Huiginn B, Bailey L, Birol I, et al. ORCA: a comprehensive bioinformatics container environment for education and research. Bioinformatics 2019;35:4448-4450. https://doi.org/10.1093/bioinformatics/btz278
  6. Basic Algorithms of Bioinformatics Applet. Casagrande, 2022. Accessed 2022 Aug 8. Available from: http://baba.sourceforge.net/.
  7. Mount DW. Bioinformatics: Sequence and Genome Analysis. New York: Cold Spring Harbor Laboratory Press, 2001.
  8. Dhruv AJ, Patel R, Doshi N. Python: the most advanced programming language for computer science applications. In: Proceedings of the International Conference on Culture Heritage, Education, Sustainable Tourism, and Innovation Technologies (CESIT 2020). Setubal: SciTePress, Science and Technology Publications, 2021. pp. 292-299.
  9. Xu X, Chan Y, Xu K, Zhang J, Wang X, Yin Z, et al. SLPal: Accelerating long sequence alignment on many-core and multi-core architectures. In: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). New York: Institute of Electrical and Electronics Engineers, 2020.