title: Alignment of three biological sequences with an efficient traceback procedure.
abstract: The major algorithms currently used for aligning biological sequences are those based on dynamic programming method. A dynamic programming algorithm consists of two major procedures, forward and traceback routines. This paper describes a dynamic programming algorithm for aligning three sequences at a time. Deletions and insertions are penalized according to their numbers and lengths. A forward process is accomplished in O(L3) computational steps, where L is the average sequence length. On the other hand, a traceback process is done in T steps, where T is the number of elementary configurations involved in the optimal alignment (usually T much less than L). The traceback procedure uses an effective technique for memory management, which is applicable to a wide range of sequence-matching methods.
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D009696:Nucleic Acids; D011506:Proteins; D012984:Software
chemical_list: D009696:Nucleic Acids; D011506:Proteins