RT Journal Article
T1 Phylogenies from unaligned proteomes using sequence environments of amino acid residues.
A1 Aledo-Ramos, Juan Carlos
K1 Filogenia
K1 Proteómica
K1 Bioinformática
AB Alignment-free methods for sequence comparison and phylogeny inference have attracted a greatdeal of attention in recent years. Several algorithms have been implemented in diverse softwarepackages. Despite the great number of existing methods, most of them are based on word statistics.Although they propose different filtering and weighting strategies and explore different metrics, theirperformance may be limited by the phylogenetic signal preserved in these words. Herein, we presenta different approach based on the species-specific amino acid neighborhood preferences. Thesedifferential preferences can be assessed in the context of vector spaces. In this way, a distance-basedmethod to build phylogenies has been developed and implemented into an easy-to-use R package.Tests run on real-world datasets show that this method can reconstruct phylogenetic relationshipswith high accuracy, and often outperforms other alignment-free approaches. Furthermore, we presentevidence that the new method can perform reliably on datasets formed by non-orthologous proteinsequences, that is, the method not only does not require the identification of orthologous proteins,but also does not require their presence in the analyzed dataset. These results suggest that theneighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility inphylogenomics.
PB Nature Portfolio
YR 2022
FD 2022-05-06
LK https://hdl.handle.net/10630/40143
UL https://hdl.handle.net/10630/40143
LA eng
NO Aledo, J.C. Phylogenies from unaligned proteomes using sequence environments of amino acid residues. Sci Rep 12, 7497 (2022). https://doi.org/10.1038/s41598-022-11370-x
DS RIUMA. Repositorio Institucional de la Universidad de Málaga
RD 13 may 2026