Exact Pattern Matching for RNA Secondary Structures
نویسندگان
چکیده
منابع مشابه
Pattern Matching and Local Alignment for RNA Structures
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A,C,G,U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between A − U and G − C. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. This paper considers pattern matching...
متن کاملExact matching of RNA secondary structure patterns
Many RNA structures are assembled from a collection of RNA motifs, which appear repeatedly and in various combinations. Identification of RNA structural motifs will enhance our understanding of RNA structures and functions. Searching for secondary structural patterns in sequence databases is the basic technique and fundamental problem for extracting and identifying such motifs. A number of algo...
متن کاملAlgorithms for pattern matching and discovery in RNA secondary structure
Text-indexing structures provide significant advantages in the solution of many problems related to string analysis and comparison, and are nowadays widely used in the analysis of biological sequences. In this paper, we present some applications of affix trees to problems of exact and approximate pattern matching and discovery in RNA sequences. By allowing bidirectional search for symmetric pat...
متن کامل\recent Methods for Rna Modeling Using Stochastic Context-free Grammars," Proc. Combinatorial Pattern
Ribonucleic acid (RNA) strings are strings over the four-letter alphabet fA;C;G;Ug with a secondary structure of base-pairing between A U and C G pairs in the string 1 . Edges are drawn between two bases that are paired in the secondary structure and these edges have traditionally been assumed to be noncrossing. The noncrossing base-pairing naturally leads to a tree-like representation of the s...
متن کاملAutomated Discovery of Active Motifs in Multiple RNA Secondary Structures
In this paper we present a method for discovering approximately common motifs (also known as active motifs) in multiple RNA secondary structures. The secondary structures can be represented as ordered trees (i.e., the order among siblings matters). Motifs in these trees are connected subgraphs that can differ in both substitutions and deletions/insertions. The proposed method consists of two st...
متن کامل