Introduction

BACKGROUND: Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference. METHODS: Here, we describe a few methods that predict protein function exclusively through homology. Together, they set the bar or lower limit for future improvements. RESULTS AND CONCLUSIONS: During the development of these methods, we faced two surprises. Firstly, our most successful implementation for the baseline ranked very high at CAFA1. In fact, our best combination of homology-based methods fared only slightly worse than the top-of-the-line prediction method from the Jones group. Secondly, although the concept of homology-based inference is simple, this work revealed that the precise details of the implementation are crucial: not only did the methods span from top to bottom performers at CAFA, but also the reasons for these differences were unexpected. In this work, we also propose a new rigorous measure to compare predicted and experimental annotations. It puts more emphasis on the details of protein function than the other measures employed by CAFA and may best reflect the expectations of users. Clearly, the definition of proper goals remains one major objective for CAFA.

Publications

  1. Homology-based inference sets the bar high for protein function prediction.
    Cite this
    Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Rost B, 2013-01-01 - BMC bioinformatics

Credits

  1. Tobias Hamp
    Developer

  2. Rebecca Kassner
    Developer

  3. Stefan Seemayer
    Developer

  4. Esmeralda Vicedo
    Developer

  5. Christian Schaefer
    Developer

  6. Dominik Achten
    Developer

  7. Florian Auer
    Developer

  8. Ariane Boehm
    Developer

  9. Tatjana Braun
    Developer

  10. Maximilian Hecht
    Developer

  11. Mark Heron
    Developer

  12. Peter Hönigschmid
    Developer

  13. Thomas A Hopf
    Developer

  14. Stefanie Kaufmann
    Developer

  15. Michael Kiening
    Developer

  16. Denis Krompass
    Developer

  17. Cedric Landerer
    Developer

  18. Yannick Mahlich
    Developer

  19. Manfred Roos
    Developer

  20. Burkhard Rost
    Investigator

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Summary
AccessionBT006912
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByBurkhard Rost