Integrating AI with Sequence Analysis

This chapter will discuss one example of how AI techniques are being integrated with, and extending, existing molecular biology sequence analysis methods. AI ideas of complex representations, pattern recognition, search, and machine learning have been applied to the task of inferring and recognizing structural patterns associated with molecular function. We wish to construct such patterns, and to recognize them in unknown molecules, based on information inferred solely from protein primary (amino acid) sequences. Besides its intrinsic interest as a difficult machine learning task of induction from complex and noisy data, this is of interest in the empirical domain for: