Efficient sequence alignment algorithms

Michael S. Waterman
1984 Journal of Theoretical Biology  
Sequence alignments are becoming more important with the increase of nucleic acid data. Fitch and Smith have recently given an example where multiple insertion/deletions (rather than a series of adjacent single insertion/deletions) are necessary to achieve the correct alignment. Multiple insertionJdeletions are known to increase computation time from O( n 2 ) to O ( n 3 ) although Gotoh has presented an O(n2) algorithm in the case the multiple insertion/deletion weighting function is linear. It
more » ... is argued in this paper that it could be desirable to use concave weighting functions. For that case, an algorithm is derived that is conjectured to be O ( n 2 ) .
doi:10.1016/s0022-5193(84)80037-5 pmid:6748696 fatcat:ie4j2pbj5vhibfnalj264bdm64