A Bayesian Scoring Scheme based Particle Swarm Optimization algorithm to identify transcription factor binding sites

Enhancing of Particle Swarm Optimization Based Method for Multiple Motifs Detection in DNA Sequences Collections

Genome sequence data consists of DNA sequences or input sequences. Each one includes nucleotides with chemical structures presented as characters: ^'A^', ^'C^',^' G^', and 'T', and groups of motif sequences, called Transcription Factor Binding Sites (TFBSs), which are subsequences of DNA that lead to protein-synthesis. The detection of TFBSs is an important problem for bioinformatics research. With the similar patterns of motif sequences in TFBSs, computational algorithms for TFBSs detection have been improved to reduce resources used in laboratory setting. The metaheuristic algorithm is the important issue that has been continually improved to detect TFBSs with greater precision and recall. This paper proposes PSO_HD by applying Particle Swarm Optimization (PSO) as a pre-process and using Hamming distance to improve the efficiency of detecting TFBSs with more precision and recall. In order to measure its efficiency, the paper compares the TFBSs detection using PSO_HD algorithm with relevant algorithms in eight datasets. F-score is used as a measurement unit and compared to the related algorithms. The experimental results show that PSO_HD algorithm gives the highest average F-score, which can be indicated that the PSO_HD algorithm can improve the efficiency of detecting TFBSs with more precision and recall.

Comparative Analysis of DNA Motif Discovery Algorithms: A Systemic Review

Background:

Bioinformatics is an interdisciplinary field that combines biology and information technology to study how to deal with the biological data. The DNA motif discovery problem is the main challenge of genome biology and its importance is directly proportional to increasing sequencing technologies which produce large amounts of data. DNA motif is a repeated portion of DNA sequences of major biological interest with important structural and functional features. Motif discovery plays a vital role in the antibody-biomarker identification which is useful for diagnosis of disease and to identify Transcription Factor Binding Sites (TFBSs) that help in learning the mechanisms for regulation of gene expression. Recently, scientists discovered that the TFs have a mutation rate five times higher than the flanking sequences, so motif discovery also has a crucial role in cancer discovery.

Methods:

Over the past decades, many attempts use different algorithms to design fast and accurate motif discovery tools. These algorithms are generally classified into consensus or probabilistic approach.

Results:

Many of DNA motif discovery algorithms are time-consuming and easily trapped in a local optimum.

Conclusion:

Nature-inspired algorithms and many of combinatorial algorithms are recently proposed to overcome the problems of consensus and probabilistic approaches. This paper presents a general classification of motif discovery algorithms with new sub-categories. It also presents a summary comparison between them.