Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Holden, Todd; Tremberger, G.; Cheung, E.; Subramaniam, R.; Gadura, Nidhi; Schneider, P.; Sullivan, R.; Flamholz, A.; Lieberman, D.; Cheung, T.

doi:10.1117/12.825827

Cited by 2 publications

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“…The nucleotide bases are represented by A = 70, T = 66, C = 58, and G = 78, which correspond to the number of protons in the nucleus of an atom 24 . These numerical representations offer the ability to perform counting the occurrences of specific sequences within a larger sequence and comparing the similarity between two sequences 25 . This approach has been applied in the analysis of Rubisco protein genes, where a direct mapping using atomic numbers was employed to calculate sequence fluctuation 26 .…”

Section: Methodsmentioning

confidence: 99%

Comparative study of encoded and alignment-based methods for virus taxonomy classification

Shaukat,

Nguyen,

Hsu

et al. 2023

Sci Rep

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The emergence of viruses and their variants has made virus taxonomy more important than ever before in controlling the spread of diseases. The creation of efficient treatments and cures that target particular virus properties can be aided by understanding virus taxonomy. Alignment-based methods are commonly used for this task, but are computationally expensive and time-consuming, especially when dealing with large datasets or when detecting new virus variants is time sensitive. An alternative approach, the encoded method, has been developed that does not require prior sequence alignment and provides faster results. However, each encoded method has its own claimed accuracy. Therefore, careful evaluation and comparison of the performance of different encoded methods are essential to identify the most accurate and reliable approach for virus taxonomy classification. This study aims to address this issue by providing a comprehensive and comparative analysis of the potential of encoded methods for virus classification and phylogenetics. We compared the vectors generated for each encoded method using distance metrics to determine their similarity to alignment-based methods. The results and their validation show that K-merNV followed by CgrDft encoded methods, perform similarly to state-of-the-art multi-sequence alignment methods. This is the first study to incorporate and compare encoded methods that will facilitate future research in making more informed decisions regarding selection of a suitable method for virus taxonomy.

show abstract

Section: Methodsmentioning

confidence: 99%

Comparative study of encoded and alignment-based methods for virus taxonomy classification

Shaukat,

Nguyen,

Hsu

et al. 2023

Sci Rep

View full text Add to dashboard Cite

show abstract

Section: Atomic Numbermentioning

confidence: 99%

Comparative Study of Encoded and Alignment-Based Methods for Virus Taxonomy Classification

Shaukat

Nguyen

Hsu

et al. 2023

Preprint

View full text Add to dashboard Cite

The emergence of viruses and their variants has made virus taxonomy more important than ever before in controlling the spread of diseases. The creation of efficient treatments and cures that target particular virus properties can be aided by understanding virus taxonomy. Alignment-based methods are commonly used for this task, but are computationally expensive and time-consuming, especially when dealing with large datasets or when detecting new virus variants is time sensitive. An alternative approach, the encoded method, has been developed that does not require prior sequence alignment and provides faster results. However, each encoded method has its own claimed accuracy. Therefore, careful evaluation and comparison of the performance of different encoded methods are essential to identify the most accurate and reliable approach for virus taxonomy classification. This study aims to address this issue by providing a comprehensive and comparative analysis of the potential of encoded methods for virus classification and phylogenetics. We compared the vectors generated for each encoded method using distance metrics to determine their similarity to alignment-based methods. The results and their validation show that K-Mer followed by CgrDft encoded methods, perform similarly to state-of-the-art multi-sequence alignment methods. This is the first study to incorporate and compare encoded methods that will facilitate future research in making more informed decisions regarding selection of a suitable method for virus taxonomy.

show abstract

Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Cited by 2 publications

References 0 publications

Comparative study of encoded and alignment-based methods for virus taxonomy classification

Comparative study of encoded and alignment-based methods for virus taxonomy classification

Comparative Study of Encoded and Alignment-Based Methods for Virus Taxonomy Classification

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