Nanoanatomy Museum: Creating a Protein Family ProfileGrid Database

Abstract

ProfileGrids allow the easy visualization of very large protein multiple sequence alignments (MSAs). Conserved and especially variable regions are represented as a matrix color‐coded according to the residue frequency occurring at each column position. While databases of protein families exist (such as Pfam), there are few curated repositories of user‐generated MSAs possibly due to the lack of paradigms for visualizing large MSAs. Here we present progress toward building a database of protein family ProfileGrids that we call the Nanoanatomy Museum. Our initial dataset was the pre‐calculated MSAs of the largest protein families from the Pfam database (ranging up to 160,000+ homologs). We describe our high‐throughput method for calculating ProfileGrids with the new JProfileGrid v2.0 software. It allows rapid and automated generation of ProfileGrids due to algorithm optimization, a command‐line interface, and a new PNG image file output format. The final database will be a proof of principle for how established databases can incorporate ProfileGrids in the standard description about protein families thus replacing other visualizations such as sequence logos.