HCAtk and pyHCA: A Toolkit and Python API for the Hydrophobic Cluster Analysis of Protein Sequences

Tristan Bitard-Feildel; Isabelle Callebaut

The annotation of a protein sequence is very often the first step of many bioinformatics analyses, for 10 instance for studying the function of a gene or the evolution of organisms. Protein domain annotation 11 dominates analyses, describing a protein as a list of blocks corresponding to evolutionary and functional 12 conserved segments. Protein domain families have been extensively compiled through sequence or 13 structure similarity searches and stored in several public databases. These domain databases represent HCA toolkit (HCAtk), and its associated python API pyHCA. The package is easily installable and 23 extend our previous developed tools making use of the Hydrophobic Cluster Analysis (HCA) of protein 24 sequences [6, 8-10, 12, 24] , with new functionalities. The HCA methodology, based on a two-dimensional 25 representation of protein sequences, highlights clusters of hydrophobic amino acids making up globular 26 domains. More on the HCA methodology can be found in the supplementary materials. 27