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