Pairwise statistical significance of local sequence alignment using multiple parameter sets

Background: Accurate estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, a comparative study of pairwise statistical significance with database statistical significance was conducted. In this paper, we extend the earlier work on pairwise statistical significance by incorporating with it the use of multiple parameter sets. Results: Results for a knowledge discovery application of homology detection reveal that using multiple parameter sets for pairwise statistical significance estimates gives better coverage than using a single parameter set, at least at some error levels. Further, the results of pairwise statistical significance using multiple parameter sets are shown to be significantly better than database statistical significance estimates reported by BLAST and PSI-BLAST, and comparable and at times significantly better than SSEARCH. Using non-zero parameter set change penalty values give better performance than z...

• Type: Conference
• Year: 2008
• Where: CIKM
• Authors: Ankit Agrawal, Xiaoqiu Huang
• Keywords: CIKM 2008, Information Management, Multiple Parameter Sets, Parameter Sets, Statistical Significance