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Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(6) © Oxford University Press 2004; all rights reserved.

Applications Note

SQUARE—determining reliable regions in sequence alignments

Michael L. Tress *, Osvaldo Graña and Alfonso Valencia

CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain

Received on August 6, 2003 ; revised on November 6, 2003 ; accepted on November 7, 2003
Advance Access Publication February 5, 2004

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.

Availability: http://www.pdg.cnb.uam.es/servers/square

Contact: mtress{at}gredos.cnb.uam.es

* To whom correspondence should be addressed.


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