SQUARE (the Server for Quick Alignment Reliability Evaluation) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment.
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Tress ML, Graña O, Valencia A.
SQUARE–determining reliable regions in sequence alignments.
Bioinformatics (2004 Apr). Vol 20, Issue , 974-975