DiMA: sequence diversity dynamics analyser for viruses
1
Issued Date
2024-11-22
Resource Type
eISSN
14774054
Scopus ID
2-s2.0-85211001154
Pubmed ID
39592151
Journal Title
Briefings in bioinformatics
Volume
26
Issue
1
Rights Holder(s)
SCOPUS
Bibliographic Citation
Briefings in bioinformatics Vol.26 No.1 (2024)
Suggested Citation
Tharanga S., Ünlü E.S., Hu Y., Sjaugi M.F., Çelik M.A., Hekimoğlu H., Miotto O., Öncel M.M., Khan A.M. DiMA: sequence diversity dynamics analyser for viruses. Briefings in bioinformatics Vol.26 No.1 (2024). doi:10.1093/bib/bbae607 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/102341
Title
DiMA: sequence diversity dynamics analyser for viruses
Author's Affiliation
Corresponding Author(s)
Other Contributor(s)
Abstract
Sequence diversity is one of the major challenges in the design of diagnostic, prophylactic, and therapeutic interventions against viruses. DiMA is a novel tool that is big data-ready and designed to facilitate the dissection of sequence diversity dynamics for viruses. DiMA stands out from other diversity analysis tools by offering various unique features. DiMA provides a quantitative overview of sequence (DNA/RNA/protein) diversity by use of Shannon's entropy corrected for size bias, applied via a user-defined k-mer sliding window to an input alignment file, and each k-mer position is dissected to various diversity motifs. The motifs are defined based on the probability of distinct sequences at a given k-mer alignment position, whereby an index is the predominant sequence, while all the others are (total) variants to the index. The total variants are sub-classified into the major (most common) variant, minor variants (occurring more than once and of incidence lower than the major), and the unique (singleton) variants. DiMA allows user-defined, sequence metadata enrichment for analyses of the motifs. The application of DiMA was demonstrated for the alignment data of the relatively conserved Spike protein (2,106,985 sequences) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the relatively highly diverse pol gene (2637) of the human immunodeficiency virus-1 (HIV-1). The tool is publicly available as a web server (https://dima.bezmialem.edu.tr), as a Python library (via PyPi) and as a command line client (via GitHub).