Codifying Primary Protein Structure as Peptides Frequencies Vector An Efficient Alternative Method to Investigate Relationships among Genes and Organisms

Abstract—There are no uniquely correct methods for inferring phylogenies. In this scenario, Linear Algebra methods and visualization techniques are essential to better analyze complex systems and can be very helpful to categorize species. Thus, if proteins are represented as vectors, it will be possible to apply Linear Algebra methods in order to investigate relationships among genes and organisms. To investigate whether or not primary protein sequences and genomes can be represented as vectors and processed by Linear Algebra methods to generate accurate phylogenetic relationships, four sets of sequences were analyzed by classical phylogenetics techniques, based on pairwise multiple alignments, and by Linear Algebra and optimization methods. The results showed that primary protein sequences and genomes can be represented as vectors in multidimensional space in such way that when they are mapped into 3D space the relationships among species are consistent with classic phylogenetic trees. Keywords-protein sequences; phylogenetics; linear algebra methods. I