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© Oxford University Press

Finding steady alignments: similarity and distance

V. V. Panjukov

Research Computing Centre Pushchino, Moscow Region, 142292 Russia

Certain alignments keep the optimum despite the weight parameters varying over a range of values. Alignments of this kind are called steady. A method finding all the steady optimal alignments of two sequences is presented providing that a gap penalty is directly proportional to gap length. It has been discovered previously that a weight of <0.5 for one insertion/deletion forces the similarity and distance out of equivalence. An account for this fact is given.

Received on March 6, 1992; accepted on July 18, 1992

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