On the Dependence Structure of Sequence Alignment Scores Calculated with Multiple Scoring Matrices

Frommlet Florian and Futschik Andreas
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Frommlet Florian: Medical University of Vienna
Futschik Andreas: Univ. of Vienna

Statistical Applications in Genetics and Molecular Biology, 2004, vol. 3, issue 1, 14

Abstract: A common practice in protein sequence alignment is to try several scoring matrices until ``something interesting'' is found. This leads to a multiple testing problem making p- and E-values hard to interpret. We focus on local alignment and propose to use logistic copula functions to model explicitly the dependence structure of scores obtained using different scoring matrices. By doing this, we obtain p-value correction factors when using more than one scoring matrix on the same sequences. Furthermore the parameter of the logistic copula can be interpreted as measure of dependence, providing insight concerning the relatedness of the scores from different matrices.

Keywords: sequence alignment; copula functions; multivariate dependence (search for similar items in EconPapers)
Date: 2004
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Citations: View citations in EconPapers (1)

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DOI: 10.2202/1544-6115.1073

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