pattern matching through chaos game representation bridging numerical and discrete data structures for biological sequence analysis通过衔接混乱游戏表示数值模式匹配和离散数据结构生物序列分析.pdfVIP

Vinga et al. Algorithms for Molecular Biology 2012, 7:10 /content/7/1/10 RESEARCH Open Access Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis Susana Vinga1,2*, Alexandra M Carvalho3,4, Alexandre P Francisco1,4, Luís MS Russo1,4 and Jonas S Almeida5 Abstract Background: Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2-L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results: The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions: The analysis of biological sequences relies on algorithmic fou