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Server-Side Query Language for Protein Structure Similarity Searching

  • B. Małysiak-Mrozek
  • S. Kozielski
  • D. Mrozek
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 99)

Abstract

Protein structure similarity searching is a complex process, which is usually carried out through comparison of the given protein structure to a set of protein structures from a database. Since existing database management systems do not offer integrated exploration methods for querying protein structures, the structural similarity searching is usually performed by external tools. This often lengthens the processing time and requires additional processing steps, like adaptation of input and output data formats. In the paper, we present our extension to the SQL language, which allows to formulate queries against a database in order to find proteins having secondary structures similar to the structural pattern specified by a user. Presented query language is integrated with the relational database management system and it simplifies the manipulation of biological data.

Keywords

Secondary Structure Secondary Structure Element Query Pattern Relational Database Management System Protein Structure Similarity 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • B. Małysiak-Mrozek
    • 1
  • S. Kozielski
    • 1
  • D. Mrozek
    • 1
  1. 1.Institute of InformaticsSilesian University of TechnologyGliwicePoland

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