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.
Stojmirović
Aleksandar
A
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
Yu
Yi-Kuo
YK
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D017385:Sequence Homology