Selection of a Consensus Area Size for Multithreaded Wavefront-Based Alignment Procedure for Compressed Sequences of Protein Secondary Structures.

Multithreaded wavefront-based alignment procedure is used in the PSS-SQL language that allows for flexible scanning of databases of protein secondary structures and finding similarities among protein molecules. Efficiency of the process depends on several factors, including the way how the similarity matrix, calculated during the process, is divided into areas, the number of CPU cores possessed by the computer hosting the database with PSS-SQL extension, and structural patterns submitted by users in PSS-SQL queries. In this paper, we show how we achieved consensus values of area sizes for the multithreaded wavefront-based alignment procedure by a series of experimental trials. Availability: PSS-SQL extension for Microsoft SQL Server database management system can be downloaded from PSS-SQL project home page available at: http://www.zti.aei.polsl.pl/w3/dmrozek/science/pss-sql.htm.