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- W2274450123 abstract "A discrete mathematical method, Boolean analysis (or BOOL-AN), was used for evaluating of functional relationships within and between the families of transfer RNA sequences. The binary encoded sequence information of each transfer RNA was transformed into a compact analytical form, called the Iterative Canonical Form (ICF) of Boolean functions. This canonical form can also be represented as a non-complete bipartite graph and used then as a generalized molecular descriptor. What is important ICF graphs can be derived without restrictions concerning the number of nodes. Besides, the proposed molecular descriptors are unique, compact, and complete, allowing sequence reconstruction without loss of information. The method provides raw vector data for calculating distance matrices by using different metrics. In turn, the calculated distances can be analyzed by neighbor-joining or by unweighted pair group method to derive a tree, or by principal coordinates analysis to obtain a multidimensional scaling plot. The ability to arrange the functionally identical tRNA isoacceptors into exclusive groups, reflecting the relationships between 22 tRNA sets with different amino acid specificities, was tested on tRNA genes of Escherichia coli. Performance of the BOOL-AN was compared with other methods, including standard phylogenetic approaches and distance calculations, based on DNA sequences and chemical indices. The results of classification are represented by trees. We conclude that ICF-graph distance calculations and the BOOL-AN software were able to derive the most consistent tree for tRNA isoacceptors in comparison with other methods. Copyright © 2016 John Wiley & Sons, Ltd." @default.
- W2274450123 created "2016-06-24" @default.
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- W2274450123 date "2016-02-17" @default.
- W2274450123 modified "2023-10-18" @default.
- W2274450123 title "Classification of tRNA isoacceptor sequences by using graph-based molecular descriptors" @default.
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- W2274450123 doi "https://doi.org/10.1002/cem.2781" @default.
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