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CSA is a web server for the comprehensive comparison of pairwise proteinstructure alignments. Its exact alignment engine computes either optimal,top-scoring alignments or heuristic alignments with quality guarantee for theinter-residue distance based scorings of contact map overlap, PAUL, DALI andMATRAS. These and additional, uploaded alignments are compared using a numberof quality measures and intuitive visualizations. CSA brings new insight intothe structural relationship of the protein pairs under investigation and is avaluable tool for studying structural similarities. It is available athttp://csa.project.cwi.nl

CSA: Comprehensive comparison of pairwise protein structure alignments