Logarithmic gap costs decrease alignment accuracy

Cartwright, Reed A

doi:10.1186/1471-2105-7-527

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Logarithmic gap costs decrease alignment accuracy.

Published in BMC bioinformatics • Dec 5, 2006

Authors:

Reed A Cartwright

Abstract

BACKGROUND: Studies on the distribution of indel sizes have consistently found that they obey a power law. This finding has lead several scientists to propose that logarithmic gap costs, G (k) = a + c ln k, are more biologically realistic than affine gap costs, G (k) = a + bk, for sequence alignment...

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