A metric for rooted trees with unlabeled vertices based on nested parentheses
Theoretical Computer Science
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We point out the importance to incorporate affinegappenalties in RNA secondary-structure comparison. Twonotions of affine-gap penalties, one for sequences and the otherfor structures, are developed. A model from Jiang et al. in [JComput Biol, 2002, 9, (2), pp. 371–388] is extended to allowthis facility, and a polynomial-time algorithm is provided inthis paper. Experimental results in this paper revealed that ournew model generates more accurate and biological meaningfulalignments than several existing algorithms.