RNA secondary structure comparison: exact analysis of the Zhang-Shasha tree edit algorithm
نویسندگان
چکیده
منابع مشابه
A new constrained edit distance between quotiented ordered trees
In this paper we propose a dynamic programming algorithm to compare two quotiented ordered trees using a constrained edit distance. An ordered tree is a tree in which the left-to-right order among siblings is significant. A quotiented ordered tree is an ordered tree T with an equivalence relation on vertices and such that, when the equivalence classes are collapsed to super-nodes, the graph so ...
متن کاملComparing RNA structures using a full set of biologically relevant edit operations is intractable
Arc-annotated sequences are useful for representing structural information of RNAs and have been extensively used for comparing RNA structures in both terms of sequence and structural similarities. Among the many paradigms referring to arcannotated sequences and RNA structures comparison (see (Blin et al. 2008) for more details), the most important one is the general edit distance. The problem ...
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An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of transforming one tree into the other through a sequence of edit operations. We present techniques for speeding up the tree edit distance computation which are applicable to a family of algorithms based...
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Ordered labeled trees are trees in which the left-to-right order among siblings is. significant. The distance between two ordered trees is considered to be the weighted number of edit operations (insert, delete, and modify) to transform one tree to another. The problem of approximate tree matching is also considered. Specifically, algorithms are designed to answer the following kinds of questio...
متن کاملTree Edit Distance Problems: Algorithms and Applications to Bioinformatics
Tree structured data often appear in bioinformatics. For example, glycans, RNA secondary structures and phylogenetic trees usually have tree structures. Comparison of trees is one of fundamental tasks in analysis of these data. Various distance measures have been proposed and utilized for comparison of trees, among which extensive studies have been done on tree edit distance. In this paper, we ...
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ورودعنوان ژورنال:
- Theor. Comput. Sci.
دوره 306 شماره
صفحات -
تاریخ انتشار 2003