Amino acid stylization: a new approach for representing protein sequences and scoring protein alignments

Abstract

SynopsisThe amino acids (AA) stylization, introduced in this work, is a mean to obtain a qualitative and quantitative description of different AA; the goal is to allow, via a chemically meaningful representation, the analysis of protein similarity in multiple alignments, without any statistical and evolutionary information involved. The AA Stylization Matrix Method (aSMM) has been tested positively with different data sets, in line with most common statistically based approaches (e.g. BLOSUM62), while allowing the exploitation of some unique capabilities, e.g. to be rapidly configured for specific properties that can be (over-, or under-) weighted. Overall, applying ad hoc parameterization aSMM permits a tailored investigation to account for different types of substitutions in protein alignments.