disclosed is a computational method for predicting intramolecular and intermolecular biopolymer interactions which provides an improved way of determining structure and function information , including intramolecular and intermolecular interactions using an ab initio - type approach , i . e . using only sequence information . the method is a widely applicable sequence - mining tool capable of detecting both intramolecular and intermolecular interactions for all biopolymers , including , but not limited to , dna , rna and protein . it possesses an adaptive screening process that allows for high accuracy . it can be an entirely rule - free , unbiased methodology , and thus can detect novel interactions for all biopolymers . due to the incorporation of a misalignment process , it can be used iteratively and is capable of refining its own predictions and detecting and managing errors . therefore , the disclosed method also provides a technique for more accurately determining sequence alignments .