An efficient and flexible scanning of databases of protein secondary structures
| العنوان: | An efficient and flexible scanning of databases of protein secondary structures |
|---|---|
| المؤلفون: | Stanisław Kozielski, Bożena Małysiak-Mrozek, Bartek Socha, Dariusz Mrozek |
| المصدر: | Journal of Intelligent Information Systems. 46:213-233 |
| بيانات النشر: | Springer Science and Business Media LLC, 2015. |
| سنة النشر: | 2015 |
| مصطلحات موضوعية: | 0301 basic medicine, Protein structure database, SQL, Database, Computer Networks and Communications, Relational database, Programming language, Computer science, Data definition language, computer.software_genre, Query language, 03 medical and health sciences, 030104 developmental biology, Relational database management system, Artificial Intelligence, Hardware and Architecture, Query by Example, Sargable, computer, Software, Information Systems, computer.programming_language |
| الوصف: | Protein secondary structure describe protein construction in terms of regular spatial shapes, including alpha-helices, beta-strands, and loops, which protein amino acid chain can adopt in some of its regions. This information is supportive for protein classification, functional annotation, and 3D structure prediction. The relevance of this information and the scope of its practical applications cause the requirement for its effective storage and processing. Relational databases, widely-used in commercial systems in recent years, are one of the serious alternatives honed by years of experience, enriched with developed technologies, equipped with the declarative SQL query language, and accepted by the large community of programmers. Unfortunately, relational database management systems are not designed for efficient storage and processing of biological data, such as protein secondary structures. In this paper, we present a new search method implemented in the search engine of the PSS-SQL language. The PSS-SQL 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 paper, we will show how the search process can be accelerated by multiple scanning of the Segment Index and parallel implementation of the alignment procedure using multiple threads working on multiple-core CPUs. |
| تدمد: | 1573-7675 0925-9902 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_________::ba90720eff24f2980159c7cf104722e2Test https://doi.org/10.1007/s10844-014-0353-0Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi...........ba90720eff24f2980159c7cf104722e2 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15737675 09259902 |
|---|