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

ABSTRACT:

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

SUBMITTER: Sadreyev RI 

PROVIDER: S-EPMC516024 | biostudies-literature | 2004 Aug

REPOSITORIES: biostudies-literature