Abstract:
:There are a few algorithms designed to solve the problem of the optimal alignment of one sequence, the pattern, of length m, with another, longer sequence the text, of length n. These algorithms allow mismatches, deletions and insertions. Algorithms to date run in O(mn) time. Let us define an integer, k, which is the maximal number of differences allowed. We present a simple algorithm showing that sequences can be optimally aligned in O(k2n) time. For long sequences the gain factor over the currently used algorithms is very large.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Landau GM,Vishkin U,Nussinov Rdoi
10.1093/nar/14.1.31subject
Has Abstractpub_date
1986-01-10 00:00:00pages
31-46issue
1eissn
0305-1048issn
1362-4962journal_volume
14pub_type
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