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RBT-GA: a novel metaheuristic for solving the Multiple Sequence Alignment problem.

ABSTRACT: BACKGROUND: Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins in order to investigate the underlying main characteristics/functions. This information is also used to generate phylogenetic trees. RESULTS: This paper presents a novel approach, namely RBT-GA, to solve the MSA problem using a hybrid solution methodology combining the Rubber Band Technique (RBT) and the Genetic Algorithm (GA) metaheuristic. RBT is inspired by the behavior of an elastic Rubber Band (RB) on a plate with several poles, which is analogues to locations in the input sequences that could potentially be biologically related. A GA attempts to mimic the evolutionary processes of life in order to locate optimal solutions in an often very complex landscape. RBT-GA is a population based optimization algorithm designed to find the optimal alignment for a set of input protein sequences. In this novel technique, each alignment answer is modeled as a chromosome consisting of several poles in the RBT framework. These poles resemble locations in the input sequences that are most likely to be correlated and/or biologically related. A GA-based optimization process improves these chromosomes gradually yielding a set of mostly optimal answers for the MSA problem. CONCLUSION: RBT-GA is tested with one of the well-known benchmarks suites (BALiBASE 2.0) in this area. The obtained results show that the superiority of the proposed technique even in the case of formidable sequences.

SUBMITTER: Taheri J

PROVIDER: S-EPMC2709253 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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RBT-GA: a novel metaheuristic for solving the Multiple Sequence Alignment problem.

Taheri Javid J Zomaya Albert Y AY

BMC genomics 20090707

<h4>Background</h4>Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins in order to investigate the underlying main characteristics/functions. This information is also used to generate phylogenetic trees.<h4>Results</h4>This paper presents a novel approach, namely RBT-GA, to solve the MSA problem using a hybrid solution methodology combining ...[more]

PMID: 19594869

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Project description:In this paper we argue that a synthesis of findings across the various sub-areas of research in complex problem solving and consequently progress in theory building is hampered by an insufficient differentiation of complexity and difficulty. In the proposed framework of person, task, and situation (PTS), complexity is conceptualized as a quality that is determined by the cognitive demands that the characteristics of the task and the situation impose. Difficulty represents the quantifiable level of a person's success in dealing with such demands. We use the well-documented "semantic effect" as an exemplar for testing some of the conceptual assumptions derived from the PTS framework. We demonstrate how a differentiation between complexity and difficulty can help take beyond a potentially too narrowly defined psychometric perspective and subsequently gain a better understanding of the cognitive mechanisms behind this effect. In an empirical study a total of 240 university students were randomly allocated to one of four conditions. The four conditions resulted from contrasting the semanticity level of the variable labels used in the CPS system (high vs. low) and two instruction conditions for how to explore the CPS system's causal structure (starting with the assumption that all relationships between variables existed vs. starting with the assumption that none of the relationships existed). The variation in the instruction aimed at inducing knowledge acquisition processes of either (1) systematic elimination of presumptions, or (2) systematic compilation of a mental representation of the causal structure underpinning the system. Results indicate that (a) it is more complex to adopt a "blank slate" perspective under high semanticity as it requires processes of inhibiting prior assumptions, and (b) it seems more difficult to employ a systematic heuristic when testing against presumptions. In combination, situational characteristics, such as the semanticity of variable labels, have the potential to trigger qualitatively different tasks. Failing to differentiate between 'task' and 'situation' as independent sources of complexity and treating complexity and difficulty synonymously threaten the validity of performance scores obtained in CPS research.

Dataset Information

RBT-GA: a novel metaheuristic for solving the Multiple Sequence Alignment problem.

Publications

RBT-GA: a novel metaheuristic for solving the Multiple Sequence Alignment problem.

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