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Abstract: In this paper, we consider PLAINS, an algorithm that provides efficient alignment over DNA sequences using piecewise-linear gap penalties that closely approximate more general and meaningful gap-functions. The innovations of PLAINS are fourfold. First, when the number of parts to a piecewise-linear gap function is fixed, PLAINS uses linear space in the worst case, and obtains an alignment that is provably correct under its memory constraints, and thus has an asymptotic complexity similar to... (Update)
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BibTeX entry: (Update)
@misc{ practical-aligning,
author = "Plains Algorithm Practical",
title = "Aligning Sequences with Non-Affine Gap Penalty:",
url = "citeseer.ist.psu.edu/765700.html" }
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