About

Raw DNA sequences, which consist of long strings of bases, are hard for humans to make sense of at a glance. However, there is significant biological meaning contained within. To reveal this meaning, a number of methods have been proposed to convert raw DNA sequences into two-dimensional visualizations. This website allows you to try several of these methods out on your in your browser. No data leaves your computer, thanks to the power of WebAssembly!

If you use this tool in your research, please cite it as:

Benjamin D. Lee, Michael A. Timony, Pablo Ruiz, DNAvisualization.org: a serverless web tool for DNA sequence visualization, Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W20–W25, https://doi.org/10.1093/nar/gkz404

Alternatively, if BibTeX is your style:

@article{10.1093/nar/gkz404,
    author = {Lee, Benjamin D and Timony, Michael A and Ruiz, Pablo},
    title = "{DNAvisualization.org: a serverless web tool for DNA sequence visualization}",
    journal = {Nucleic Acids Research},
    volume = {47},
    number = {W1},
    pages = {W20-W25},
    year = {2019},
    month = {06},
    issn = {0305-1048},
    doi = {10.1093/nar/gkz404},
    url = {https://doi.org/10.1093/nar/gkz404},
    eprint = {https://academic.oup.com/nar/article-pdf/47/W1/W20/28879727/gkz404.pdf},
}

Citations of DNAvisualization.org

For the most recent list of citations, take a look at our Google Scholar page. Here are a few:

  • Niu, Xingzhi, et al. "Leveraging serverless computing to improve performance for sequence comparison." Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. 2019.
  • Shafiei, Hossein, Ahmad Khonsari, and Payam Mousavi. "Serverless computing: A survey of opportunities, challenges and applications." (2020).
  • Malla, Sulav, and Ken Christensen. "HPC in the cloud: Performance comparison of function as a service (FaaS) vs infrastructure as a service (IaaS)." Internet Technology Letters 3.1 (2020): e137.
  • Veldsman, Werner P., et al. "Characterization of the complete mitochondrial genome of a coconut crab, Birgus latro (Linnaeus, 1767)(Decapoda: Anomura: Coenobitidae), from Okinawa, Japan." Journal of Crustacean Biology (2020).
  • Khandelwal, Anurag, Arun Kejariwal, and Karthikeyan Ramasamy. "Le Taureau: Deconstructing the Serverless Landscape & A Look Forward." Proceedings of the 2020 ACM SIGMOD International Conference on Management of Data. 2020.
  • Temple, Mark D. "Real-time audio and visual display of the Coronavirus genome." (2020).

Methods Reference

For references for the supported methods, please look here:

Squiggle

If you use the Squiggle visualization method, please cite the following paper (full text):

  • Lee, B. D. (2018). Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. Bioinformatics. doi:10.1093/bioinformatics/bty807.
Yau

If you use the Yau visualization method, please cite the following paper (full text):

  • Yau, S. S., Wang, J., Niknejad, A., Lu, C., Jin, N., & Ho, Y. K. (2003). DNA sequence representation without degeneracy. Nucleic acids research, 31(12), 3078-80.
Randić

If you use the Randic visualization method, please cite the following paper:

  • Randić, M., Vračko, M., Lerš, N., & Plavšić, D. (2003). Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chemical Physics Letters, 368(1–2), 1–6. doi:10.1016/s0009-2614(02)01784-0.
Qi

If you use the Qi visualization method, please cite the following paper:

  • Qi, Z., & Qi, X. (2007). Novel 2D graphical representation of DNA sequence based on dual nucleotides. Chemical Physics Letters, 440(1–3), 139–144. doi:10.1016/j.cplett.2007.03.107.