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BMCBI
2004

Estimates of statistical significance for comparison of individual positions in multiple sequence alignments

9 years 8 months ago
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments
Background: Profile-based analysis of multiple sequence alignments (MSA) allows for accurate comparison of protein families. Here, we address the problems of detecting statistically confident dissimilarities between (1) MSA position and a set of predicted residue frequencies, and (2) between two MSA positions. These problems are important for (i) evaluation and optimization of methods predicting residue occurrence at protein positions; (ii) detection of potentially misaligned regions in automatically produced alignments and their further refinement; and (iii) detection of sites that determine functional or structural specificity in two related families. Results: For problems (1) and (2), we propose analytical estimates of P-value and apply them to the detection of significant positional dissimilarities in various experimental situations. (a) We compare structure-based predictions of residue propensities at a protein position to the actual residue frequencies in the MSA of homologs. (b...
Ruslan Sadreyev, Nick V. Grishin
Added 16 Dec 2010
Updated 16 Dec 2010
Type Journal
Year 2004
Where BMCBI
Authors Ruslan Sadreyev, Nick V. Grishin
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