Sequence alignment from the perspective of stochastic optimization: a survey

DNA and protein are the fundamental biological sequences. DNA is a fundamental molecule that plays a vital role in the processes of life. Proteins synthesized by DNA in a cell are the building blocks of every living organism. There is a variety of reasons behind the alignment of biological sequences...

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Bibliographic Details
Published in:Elektrik : Turkish journal of electrical engineering & computer sciences 2011, Vol.19 (1), p.157-173
Main Authors: BUCAK, İhsan Ömür, USLAN, Volkan
Format: Article
Language:English
Subjects:
Ant colony optimization
Benzetim tavlaması
Dizinsel hizalama
genetic algorithm
Genetik algoritma
İşletme Mühendisliği
Karınca kolonisi optimizasyonu
Management Engineering
Particle swarm optimization
Parçacık sürü optimizasyonu
sequence alignment
simulated annealing
Stochastic optimization
Stokastik optimizasyon
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Summary:DNA and protein are the fundamental biological sequences. DNA is a fundamental molecule that plays a vital role in the processes of life. Proteins synthesized by DNA in a cell are the building blocks of every living organism. There is a variety of reasons behind the alignment of biological sequences. Biological sequence alignment helps to discover functional and structural similarity of sequences. Biologists work with these aligned sequences to construct phylogenetic trees, characterize protein families, and predict protein structure. Sequence alignment is an extremely promising field of research that is characterized by very high computational complexity. Stochastic optimization is needed for sequence alignment, as it generates efficient solutions to the problem. The objective of this study is to survey recent trends in stochastic optimization for sequence alignment as means of a guide for researchers who are interested in the sequence alignment problem.
ISSN:1300-0632
DOI:10.3906/elk-1002-410