Searching on the Secondary Structure of Protein Sequences

In spite of the many decades of progress in database research, surprisingly scientists in the life sciences community still struggle with inefficient and awkward tools for querying biological data sets. This work highlights a specific problem involving searching large volumes of protein data sets based on their secondary structure. In this paper we define an intuitive query language that can be used to express queries on secondary structure and develop several algorithms for evaluating these queries. We implement these algorithms both in Periscope, a native system that we have built, and in a commercial ORDBMS. We show that the choice of algorithms can have a significant impact on query performance. As part of the Periscope implementation we have also developed a framework for optimizing these queries and for accurately estimating the costs of the various query evaluation plans. Our performance studies show that the proposed techniques are very efficient in the Periscope system and ca...

• Type: Journal
• Year: 2002
• Where: VLDB
• Authors: Laurie Hammel, Jignesh M. Patel
• Keywords: Data Sets, Database, Protein Data, Secondary Structure, VLDB 2002