Finding steady alignments: similarity and distance.
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.
Panjukov
V V
VV
Research Computing Centre, Pushchino, Moscow Region, Russia.
D000465:Algorithms; D008958:Models, Molecular; D016415:Sequence Alignment / Q000379:methods*