Overall architecture of MIMOX MIMOX was coded with Perl using modules from the Bioperl [18] project. The whole online service provided by MIMOX is accomplished through a set of CGI scripts. The MIMOX service can be divided into two main sections. In the first section, MIMOX provides a simple interface for ClustalW [19] to align a set of mimotope sequences; this is implemented as the script mimosa.pl. The alignment can then be used to derive the consensus sequence through a simple statistical method; this is implemented as the script mimocs.pl. The alignment can also be viewed and managed through an embedded Java applet version of JalView [20] ; this is implemented as the script jalviews.pl. In the second section, MIMOX tries to map the user supplied sequence on to the given antigen structure. This is implemented as the script mimox.pl. The program NAC-CESS [21] is also wrapped into mimox.pl and used to calculate the surface accessibility of the mapping results. All mapping results are ranked based on their solvent accessible surface. Each mapping result has detailed information of the accessibility of each candidate residue, which is parsed through the script parsa.pl and displayed as a table in a new window. Each mapping result can also be viewed interactively on the antigen structure. This is implemented as the script jmol.pl, which wraps a Java applet version of Jmol [22] . The overall architecture of MIMOX is shown schematically in Figure 1 .