Summary: The Server for Quick Alignment Reliability Evaluation (SQUARE) 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. SQUARE produces a graphical output of the residue profile-derived alignment scores along with an indication of the reliability of the alignment. In addition, the scores can be compared against template secondary structure, conserved residues and important sites.#R##N##R##N#Availability: http://www.pdg.cnb.uam.es/servers/square
['Michael L. Tress', 'Osvaldo Graòa', 'Alfonso Valencia']
SQUARE---determining reliable regions in sequence alignments