title: SQUARE--determining reliable regions in sequence alignments.
abstract: 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.
authors.affiliation: CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain. mtress@gredos.cnb.uam.es
authors.forename: Michael L
authors.initials: ML
authors.lastname: Tress
authors.forename: Osvaldo
authors.initials: O
authors.lastname: Graña
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins