Genome Methods Applied to Reverse-Engineering

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."

Comments

Re:Bioinformatics links

[Anonymous Coward]

And apparently more proteins can be encoded than the number of genes, because of alternate orderings (counting from different displacements in the gene, I think, ask a real bioinformatics expert).

Actually, the increase in number of genes compared to actual encoded genes as you move up the "eukaryotic evolutionary chain" is due to the organisms finding new and novel ways to combine the same protiens.. not in different displacements of the same gene. See Nature paper on draft human genome analysis: Nature. 2001 Feb 15;409(6822):860-921 Also the draft Mouse genome analysis: Nature. 2002 Dec 5;420(6915):520-62