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Bioinformatics Vol. 18 no. 3 2002
Pages 496-497
© 2002 Oxford University Press

Applications Note

CASA: a server for the critical assessment of protein sequence alignment accuracy

Robel Y. Kahsay 1, Guoli Wang 2, Nataraj Dongre 1, Guang Gao 1 and Roland L. Dunbrack, Jr 2,*

1 Delaware Biotechnology Institute and Department of Electrical and Computer Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
2 Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA

Received on September 28, 2001 ; revised on November 1, 2001 ; accepted on November 7, 2001

Summary: A public server for evaluating the accuracy of protein sequence alignment methods is presented. CASA is an implementation of the alignment accuracy benchmark presented by Sauder et al. (Proteins, 40, 6–22, 2000). The benchmark currently contains 39321 pairwise protein structure alignments produced with the CE program from SCOP domain definitions. The server produces graphical and tabular comparisons of the accuracy of a user’s input sequence alignments with other commonly used programs, such as BLAST, PSI-BLAST, Clustal W, and SAM-T99.

Availability: The server is located at http://capb.dbi.udel.edu/casa.

Contact: RL_ Dunbrack{at}fccc.edu

* To whom correspondence should be addressed.


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