Patterny: A Troupe of Decipherment Helpers for Intrinsic Disorder, Low Complexity and Compositional Bias in Proteins.

Abstract

Intrinsically disordered regions (IDRs) are sometimes considered parts of the 'dark proteomes', i.e., protein parts that have been largely under-appreciated, as are the overlapping phenomena of low-complexity or compositionally biased regions (LCRs/CBRs). Experimentalists and computationalists alike are still learning how to decrypt the functionally meaningful features of such regions. Here, I report the creation of the support troupe Patterny to aid such protein cryptanalysis. The current troupe members are named Blocky, Bandy, Moduley, Repeaty, and Runny. To discern important features, protein regions are compared to ideal assortments wherein everything is sampled proportionally and dispersed randomly. Blocky discerns the segregation of amino-acids by type, and scores them for it. Bandy is focused on picking out compositional bands and calculating their evenness. Moduley labels the boundaries of optimized compositional modules ('CModules') and other possible boundary sets for compositionally biased regions. Repeaty concisely summarizes repetitiveness using an information entropy of amino-acid interval diversity. Runny enumerates homopeptide content and assesses its significance. Both original whole sequences and CModules from Moduley, are fed into the other Patterny members. Patterny is applied to some illustrative sample data from yeast proteome and the DISPROT database. It is available at Github, and might aid those aiming to intensify light-shedding and hypothesis generation for protein regions with function encoded in a distributed manner, such as IDRs and LCRs/CBRs more generally.