2.7. Co-Var web server for predicting intra- and inter molecular co-evolutionary pairings

To provide a wider scope to the Co-Var methodology, we have developed a web server version of the method which is freely accessible. Utilizing a set of homologous sequences or alignment(s) of proteins as input(s) the Co-Var methodology may be utilized for studying intra-protein or inter-protein co-evolution in our Co-Var web server available via http://www.hpppi.iicb.res.in/ishi/covar/index.html. The front end of the server is HTML, PHP and java based while a perl based implementation of the Co-Var methodology works on the backend of the server to predict reference sequence (first sequence in the alignment) mapped co-evolved residue positions. Further, based on an uploaded reference structure inter-residue distances between the co-evolutionary pairings and structural mapping of pairings can be obtained. Co-evolutionary pairings in close structural proximity can be visualized in a viewer [58]. Additional modules are available for functional interpretation of the inter-protein co-evolutionary pairings in terms of their frequency of occurrence among predicted co-evolved positions (high degree co-evolved positions). Moreover, the list of reference sequence, structure mapped, and high degree co-evolutionary pairings along with reference sequence and structure mapped residue identities can be downloaded from the mailed result link.