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January 15, 2012 (Vol. 32, No. 2)


  • Rapid analysis, simple and clear graphical results
  • Downloading instructions not obvious

What does an Octopus have to do with protein topology? Absolutely nothing, as far as I can tell. However, its caps-lock cousin OCTOPUS just so happens to be a handy tool to predict transmembrane protein structural characteristics. It does so by assigning stretches of a user-entered FASTA amino acid sequence one of four identities: membrane, interface, closed loop, or globular loop region. In a separate analysis, it also scores whether a region is more likely to be inside or outside of the cell. The output of the analysis is a simple graphical representation indicating the predicted topology. It is nothing fancy (no ribbon models, just simple lines and boxes), but it does the job. Users can easily use OCTOPUS via the website interface, although there is also an option to freely download a software version. (A warning though—it appears that users must download a number of things before the program itself will be able to run.)

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