Geometric Aspects of Biological Sequence Comparison

We introduce a geometric framework suitable for studying the relationships among biological sequences. In contrast to previous works, our formulation allows asymmetric distances (quasi-metrics), originating from uneven weighting of strings, which may induce non-trivial partial orders on sets of biosequences. The distances considered are more general than traditional generalized string edit distances. In particular, our framework enables non-trivial conversion between sequence similarities, both local and global, and distances. Our constructions apply to a wide class of scoring schemes and require much less restrictive gap penalties than the ones regularly used. Numerous examples are provided to illustrate the concepts introduced and their potential applications.