The Frontiers of Society, Science and Technology, 2020, 2(11); doi: 10.25236/FSST.2020.021109.
Zhanlin Dong
Tianjin University School of Pharmaceutical Science and Technology, Tianjin 300072, China
E-mail: [email protected]
As an important and useful technique in the field of bioinformatics, sequence logo was firstly invented by Thomas D. Schneider and R. Michael Stephens in 1990, offering an effective method to visualize the information content at each position in the sequence motif of nucleic acid or protein. In this article, the feature and principle of sequence logo are explained on a biological and statistical level. The specific operation steps to construct sequence logo are introduced. After that, in order to introduce the actual application of the technique, CodonLogo is raised as an instance that applies sequence logo to analyze codon sequence. In the end, a potential application direction aimed to SARS-CoV-2, the pathogen of COVID-19, is anticipated, covering virus genome study and important proteins (pp1ab, nsp1 to nsp16, RdRp, spike proteins) study.
Sequence logo technique, Biological and statistical level, Codonlogo
Zhanlin Dong. An Overview of Sequence Logo Technique and Potential Application Direction. The Frontiers of Society, Science and Technology (2020) Vol. 2 Issue 11: 51-57. https://doi.org/10.25236/FSST.2020.021109.
[1] Lund O., Nielsen M., Lundegaard C., Kesmir C., Brunak S (2005). Immunological Bioinformatics, The MIT Press, 2005.
[2] Dayhoff M.O., Schwartz R., Orcutt, B.C(1978).Atlas of Protein Sequence and Structure, National Biomedical Research Foundation.
[3] Henikoff S., Henikoff J.G(1992).Amino Acid Substitution Matrices from Protein Blocks, Proc Natl Acad Sci USA, vol.89, no.22, pp.10915-10919.
[4] Schneider T.D., Stephens R.M (1990). Sequence Logos: A New Way to Display Consensus Sequences, Nucleic Acids Research, vol.18, no.20, pp. 6097-6110.
[5] Sharma V., Murphy D.P., Provan G., Baranov P.V (2012). CodonLogo: A Sequence Logo-based Viewer for Codon Patterns, Bioinformatics, vol.28, no.14, pp.1935-1936.
[6] Coronaviridae Study Group of the International Committee on Taxonomy of Viruses (2020). The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology, no.5, pp.536-544.
[7] Nagy P.D., Pogany J (2012).The Dependence of Viral RNA Replication on Co-opted Host Factors, Nat Rev Microbiol, vol.10, no.2, pp.137-149.
[8] Fehr A.R., Perlman S (2015).Coronaviruses: Methods and Protocols, Humana Press.
[9] Huang J.S., Song W.L, Huang H (2020). Pharmacological Therapeutics Targeting RNA-Dependent RNA Polymerase, Proteinase and Spike Protein: From Mechanistic Studies to Clinical Trials for COVID-19, Journal of Clinical Medicine, vol.9, no.4, pp.1131.
[10] Zhang J.Y., Zeng H., Gu J., Li H.B (2020). Progress and Prospects on Vaccine Development against SARS-CoV-2, Vaccines, vol.8, no.2, pp.153-154.