L1TH10N writes "Wired news has an article on a truely innovative way of analysing network protocol reverse-engineering. Marshall Beddoe, a security analyst, is using algorithms used in bioinformatics to analyse closed-source and secret network protocols which he calls "Protocol Informatics".According to Beddoe, network conversations are full of "junk" -- usually the actual data being sent -- which interferes with the analysis of the occasional command sequence that controls what to do with that junk. This has parrallels with Bioinformatics that has to deal with a similar problem of finding known DNA sequences separated by long gaps of unknown data. Biologists have devised complex algorithms to discover whether DNA sequences are descended from the same ancestors by comparing the genetic differences with the known mutation rates of certain DNA components. Beddoe applied the same principles to mutating network conversations of evolving network protocols."
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