On Suboptimal Alignments of Biological Sequences

It is widely accepted that the optimal alignment between a pair of proteins or nucleic acid sequences that minimizes the edit distance may not necessarily re ect the correct biologicalalignment. Alignments of proteins based on their structures or of DNA sequences based on evolutionary changes are often dierent from alignments that minimize edit distance. However, in many cases (e.g. when the sequences are close), the edit distance alignment is a good approximation to the biological one. Since, for most sequences, the true alignment is unknown, a method that either assesses the signicance of the optimal alignment, or that provides few \close" alternatives to the optimal one, is of great importance. A suboptimal alignment is an alignment whose score lies within the neighborhood of the optimal score. Enumeration of suboptimal alignments [Wa83, WaBy] is not very practical since there are many such alignments. Other approaches [Zuk, Vi, ViAr] that use only partial information about s...

• Type: Conference
• Year: 1993
• Where: CPM
• Authors: Dalit Naor, Douglas L. Brutlag
• Keywords: Combinatorics, CPM 1993, Edit Distance, Optimal Score, Suboptimal Alignments