An Alignment Algorithm for Sequences
  This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or other considerations. The algorithm does not use similarity tables and it performs aspects of both global and local alignment. The algorithm is compared with other sequence alignment algorithms. 
Sandeep Hosangadi and Subhash Kak
cs.IT math.IT