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Bioinformatics Advance Access originally published online on September 3, 2004
Bioinformatics 2005 21(3):393-395; doi:10.1093/bioinformatics/bti013
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Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.

The SSEA server for protein secondary structure alignment

Paolo Fontana 1, Eckart Bindewald 2,{dagger}, Stefano Toppo 3, Riccardo Velasco 1, Giorgio Valle 4 and Silvio C. E. Tosatto 4,*

1 Istituto Agrario di San Michele all'Adige via E. Mach 1, 38010 S.Michele all'Adige (TN), Italy
2 Center of Excellence in Bioinformatics, State University of New York at Buffalo USA
3 Department of Biological Chemistry, University of Padova V.le G. Colombo 3, 35121 Padova, Italy
4 Department of Biology and CRIBI Biotechnology Centre, University of Padova V.le G. Colombo 3, 35121 Padova, Italy

*To whom correspondence should be addressed.

Summary: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a library of domain folds. It can calculate global and local secondary structure element alignments. A combination of local and global alignment steps can be used to search for domains inside the query sequence or help in the discrimination of novel folds. Both the SCOP and PDB fold libraries, clustered at 95 and 40% sequence identity, are available for alignment.

Availability: The web server interface is freely accessible to academic users at http://protein.cribi.unipd.it/ssea/. The executable version and benchmarking data are available from the same web page.

Contact: silvio{at}cribi.unipd.it


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