Soft Ngram representation and modeling for protein remote homology detection

Remote homology detection represents a central problem in bioinformatics, where the challenge is to detect functionally related proteins when their sequence similarity is low. Recent solutions employ representations derived from the sequence profile, obtained by replacing each amino acid of the sequence by the corresponding most probable amino acid in the profile. However, the information contained in the profile could be exploited more deeply, provided that there is a representation able to capture and properly model such crucial evolutionary information. In this paper we propose a novel profile-based representation for sequences, called soft Ngram. This representation, which extends the traditional Ngram scheme (obtained by grouping N consecutive amino acids), permits to consider all of the evolutionary information in the profile: this is achieved by extracting Ngrams from the whole profile,equipping them with a weight directly computed from the corresponding evolutionary frequencies. We illustrate two different approaches to model the proposed representation and to derive a feature vector, which can be effectively used for classification using a support vector machine (SVM). A thorough evaluation on three benchmarks demonstrates that the new approach outperforms other Ngram-based methods, and shows very promising results also in comparison with a broader spectrum of techniques.