The SSEA server for protein secondary structure alignment

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.