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High-Performance Computational Solutions in Protein BioinformaticsMultithreaded PSS-SQL for Searching Databases of Secondary Structures

High-Performance Computational Solutions in Protein Bioinformatics: Multithreaded PSS-SQL for... [Protein secondary structure (PSS), as an organizational level, provides important information regarding protein construction and regular spatial shapes, including alpha-helices, beta-strands, and loops, which protein amino acid chain can adopt in some of its regions. The relevance of this information and the scope of its practical applications cause the requirement for its effective storage and processing. In this chapter, we will see how PSSs can be stored in the relational database and processed with the use of the protein secondary structure-structured query language (PSS-SQL). The PSS-SQL is an extension to the SQL language. It allows formulation of queries against a relational database in order to find proteins having secondary structures similar to the structural pattern specified by a user. In this chapter, we will see how this process can be accelerated by parallel implementation of the alignment using multiple threads working on multiple-core CPUs.] http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png

High-Performance Computational Solutions in Protein BioinformaticsMultithreaded PSS-SQL for Searching Databases of Secondary Structures

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Publisher
Springer International Publishing
Copyright
© The Author(s) 2014
ISBN
978-3-319-06970-8
Pages
25 –47
DOI
10.1007/978-3-319-06971-5_2
Publisher site
See Chapter on Publisher Site

Abstract

[Protein secondary structure (PSS), as an organizational level, provides important information regarding protein construction and regular spatial shapes, including alpha-helices, beta-strands, and loops, which protein amino acid chain can adopt in some of its regions. The relevance of this information and the scope of its practical applications cause the requirement for its effective storage and processing. In this chapter, we will see how PSSs can be stored in the relational database and processed with the use of the protein secondary structure-structured query language (PSS-SQL). The PSS-SQL is an extension to the SQL language. It allows formulation of queries against a relational database in order to find proteins having secondary structures similar to the structural pattern specified by a user. In this chapter, we will see how this process can be accelerated by parallel implementation of the alignment using multiple threads working on multiple-core CPUs.]

Published: Jun 5, 2014

Keywords: Proteins; Secondary structure; Query language; SQL; Relational database; Multithreading; Parallel computing; Alignment

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