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Bioinformatics Advance Access published online on September 3, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti013
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received March 24, 2004
Revised August 11, 2004
Accepted August 29, 2004

Applications note

The SSEA server for protein secondary structure alignment

Paolo Fontana 1, Eckart Bindewald 2, 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 Dept. of Biological Chemistry, University of Padova, V.le G. Colombo 3, 35121 Padova, Italy
4 Dept. of Biology and CRIBI Biotechnology Centre, University of Padova, V.le G. Colombo 3, 35121 Padova, Italy

* To whom correspondence should be addressed. E-mail: silvio{at}cribi.unipd.it.


  Abstract

Summary: We present a web server which 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 SCOP and the 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 from the URL: http://protein.cribi.unipd.it/ssea/. The executable version and benchmarking data are available from the same web page.


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