PSSMCOOL: a comprehensive R package for generating evolutionary-based descriptors of protein sequences from PSSM profiles

Abstract

Position-specific scoring matrix (PSSM), also called profile, is broadly used for representing the evolutionary history of a given protein sequence. Several investigations reported that the PSSM-based feature descriptors can improve the prediction of various protein attributes such as interaction, function, subcellular localization, secondary structure, disorder regions, and accessible surface area. While plenty of algorithms have been suggested for extracting evolutionary features from PSSM in recent years, there is not any integrated standalone tool for providing these descriptors. Here, we introduce PSSMCOOL, a flexible comprehensive R package that generates 38 PSSM-based feature vectors. To our best knowledge, PSSMCOOL is the first PSSM-based feature extraction tool implemented in R. With the growing demand for exploiting machine-learning algorithms in computational biology, this package would be a practical tool for machine-learning predictions.