On Suboptimal Alignments of Biological Sequences

摘要: It is widely accepted that the optimal alignment between a pair of proteins or nucleic acid sequences minimizes edit distance may not necessarily reflect correct biological alignment. Alignments based on their structures DNA evolutionary changes are often different from alignments minimize distance. However, in many cases (e.g. when close), good approximation to one. Since, for most sequences, true unknown, method either assesses significance alignment, provides few “close” alternatives one, great importance.