Trim Distance between Positions in Nucleotide Sequences for Structural Proteins of SARS-CoV-2
10th International Congress on Advanced Applied Informatics, IIAI-AAI 2021
; : 35-40, 2021.
Article
in English
| Scopus | ID: covidwho-1922696
ABSTRACT
A trim distance between two positions in the set of nucleotide sequences is a tree-based distance between the trimmed phylogenetic trees at two positions, each of which is obtained by applying the label-based closest-neighbor trimming method to the relabeled phylogenetic tree at the position that the index as a label of leaves is relabeled to the nucleotide occurring at the position. In this paper, as a tree-based distance, we adopt a label histogram distance and a depth histogram distance. Then, we introduce new trim distances that a label trim distance and a depth trim distance, respectively. Finally, by using the nucleotide sequences and the reconstructed phylogenetic tree from them provided from NCBI, we investigate the trim distances between the positions in the nucleotide sequences for structural proteins of spike, envelope, membrane and nucleocapsid proteins of SARS-CoV-2. © 2021 IEEE.
depth trim distance; label trim distance; label-based closest-neighbor trimming method; phylogenetic tree; positiions in nucleotide sequences; SARS-CoV-2; trim distance; trimmed phylogenetic tree; Bioinformatics; Graphic methods; Nucleotides; Proteins; Trees (mathematics); Trimming; Label-based close-neighbor trimming method; Nucleotides sequences; Phylogenetic trees; Positiion in nucleotide sequence; Structural proteins; Coronavirus
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Databases of international organizations
Database:
Scopus
Language:
English
Journal:
10th International Congress on Advanced Applied Informatics, IIAI-AAI 2021
Year:
2021
Document Type:
Article
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