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SQUARE--determining reliable regions in sequence alignments.

Michael L Tress·Osvaldo Graña·Alfonso Valencia
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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.

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AlgorithmsDatabases, ProteinInformation Storage and RetrievalInternetProteinsSequence AlignmentSequence Analysis, ProteinSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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BibTeXRIS

Michael L Tress, Osvaldo Graña, Alfonso Valencia. 2004-02-05. SQUARE--determining reliable regions in sequence alignments.. https://doi.org/10.1093/bioinformatics%2Fbth032

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