SQUARE—determining reliable regions in sequence alignments | Zendy

Michael L. Tress | Zendy; Osvaldo GrañaCastro | Zendy; Alfonso Valencia | Zendy

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SQUARE—determining reliable regions in sequence alignments

Author(s) -

Michael L. Tress,

Osvaldo GrañaCastro,

Alfonso Valencia

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth032

Subject(s) - sequence (biology) , computer science , square (algebra) , multiple sequence alignment , sequence alignment , sequence database , reliability (semiconductor) , web server , algorithm , data mining , mathematics , peptide sequence , biology , geometry , the internet , genetics , physics , power (physics) , quantum mechanics , world wide web , gene

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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