Metrics on RNA secondary structures

被引:69
作者
Moulton, V [1 ]
Zuker, M
Steel, M
Pointon, R
Penny, D
机构
[1] Mid Sweden Univ, FMI Phys & Math Dept, S-85170 Sundsvall, Sweden
[2] Washington Univ, Inst Biomed Comp, St Louis, MO 63110 USA
[3] Univ Canterbury, Christchurch 1, New Zealand
[4] Massey Univ, Dept Comp Sci, Palmerston North, New Zealand
[5] Massey Univ, Inst Mol BioSci, Palmerston North, New Zealand
关键词
RNA secondary structure; pseudoknot; suboptimal secondary structures; metric; distance; similarity;
D O I
10.1089/10665270050081522
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Many different programs have been developed for the prediction of the secondary structure of an RNA sequence, Some of these programs generate an ensemble of structures, all of which have free energy close to that of the optimal structure, making it important to be able to quantify how similar these different structures are. To deal with this problem, we define a new class of metrics, the mountain metrics, on the set of RNA secondary structures of a fixed length, We compare properties of these metrics with other well known metrics on RNA secondary structures. We also study some global and local properties of these metrics.
引用
收藏
页码:277 / 292
页数:16
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