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Comput Appl Biosci. 1990 Oct;6(4):309-18.

Comparing multiple RNA secondary structures using tree comparisons.

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Image Processing Section, National Cancer Institute, National Institutes of Health, Frederick, MD 21701.


In a previous paper, an algorithm was presented for analyzing multiple RNA secondary structures utilizing a multiple string alignment algorithm. In this paper we present another approach to the problem of comparing many secondary structures by utilizing a very efficient tree-matching algorithm that will compare two trees in O([T1] X [T2] X L1 X L2) in the worst case and very close to O([T1] X [T2]) for average trees representing secondary structures. The result of the pairwise comparison algorithm is then used with a cluster algorithm to produce a multiple structure clustering which can be displayed in a taxonomy tree to show related structures.

[Indexed for MEDLINE]

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