Abstract: In accordance with one embodiment of the invention, features of biological sequences are represented in a fingerprint that includes a bitset, and may also include counts, strings or continuous values, for the features. The fingerprint can be used with machine learning and statistical methods. This is especially advantageous for, though not limited to, drug discovery processes. The method permits Structure-Activity Relationship (SAR) and Quantitative Structure-Activity Relationship (QSAR) studies to be performed with biological sequences.