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Erschienen in:
Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling Kapitel lesen Erstes Kapitel lesen

2018 | OriginalPaper | Buchkapitel

11. Exploration of Protein Secondary Structures in Relational Databases with Multi-threaded PSS-SQL

verfasst von : Dariusz Mrozek

Erschienen in: Scalable Big Data Analytics for Protein Bioinformatics

Verlag: Springer International Publishing

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Abstract

Protein secondary structure reveals 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 protein secondary structures can be stored in the relational database and processed with the use of the 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 the chapter, we will see how this process can be accelerated by parallel implementation of the alignment using multiple threads working on multi-core CPUs.

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Vorheriges Kapitel Massively Parallel Searching of 3D Protein Structure Similarities on CUDA-Enabled GPU Devices
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Metadaten
Titel
Exploration of Protein Secondary Structures in Relational Databases with Multi-threaded PSS-SQL
verfasst von
Dariusz Mrozek
Copyright-Jahr
2018
Buch
Scalable Big Data Analytics for Protein Bioinformatics

Print ISBN: 978-3-319-98838-2

Electronic ISBN: 978-3-319-98839-9

Copyright-Jahr: 2018

DOI
https://doi.org/10.1007/978-3-319-98839-9_11