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Multithreaded PSS-SQL for Searching Databases of Secondary Structures

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High-Performance Computational Solutions in Protein Bioinformatics

Part of the book series: SpringerBriefs in Computer Science ((BRIEFSCOMPUTER))

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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.

...; life was no longer considered to be a result of mysterious and vague phenomena acting on organisms, but instead the consequence of numerous chemical processes made possible thanks to proteins.

Amit Kessel, Nir Ben-Tal, 2010 [13]

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  1. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Dariusz Mrozek

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  1. Dariusz Mrozek
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Mrozek, D. (2014). Multithreaded PSS-SQL for Searching Databases of Secondary Structures. In: High-Performance Computational Solutions in Protein Bioinformatics. SpringerBriefs in Computer Science. Springer, Cham. https://doi.org/10.1007/978-3-319-06971-5_2

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  • DOI: https://doi.org/10.1007/978-3-319-06971-5_2

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-06970-8

  • Online ISBN: 978-3-319-06971-5

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