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ProtoNet: charting the expanding universe of protein sequences

Nature Biotechnology volume 31, pages 290–292 (2013)Cite this article

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To the Editor:

As next-generation sequencing technologies continue to generate staggering amounts of raw protein sequences, it has become very difficult to thoroughly annotate the emerging protein-sequence space. Complete proteomes (that is, the collection of all valid proteins from a sequenced genome) as well as partial sequencing efforts have resulted in the archiving of more than 20 million protein sequences in UniProtKB (release 2012_1, 25 January 2012; http://www.uniprot.org). This repository is compiled from millions of viral sequences, thousands of microbial genomes and sequences from thousands of multicellular organisms. These sequences comprise what may be considered the now-known parts of the protein space. At present, the functional characterization available for the vast majority of this space is based mostly on sequence-similarity approaches. In fact, the characterized part of this space is orders of magnitude smaller than the whole, and only 3.5% of sequences in UniProtKB1 have any experimental support. From this view, only a robust, unsupervised and automated method can realistically achieve comprehensive and functional annotation of this rapidly expanding protein space.

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Figure 1: The ProtoNet family tree.
Figure 2: Navigating the ProtoNet tree.

References

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Acknowledgements

We thank S. Karsenty for support in design and maintenance of the ProtoNet server. We thank A. Stern for extensive analysis on the ProtoNet performance. This work was supported by an European Commission Seventh Framework Programme Prospects grant.

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Authors and Affiliations

  1. School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel

    Nadav Rappoport & Nathan Linial

  2. Department of Biological Chemistry, Institute of Life Sciences, The Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, Jerusalem, Israel

    Michal Linial

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  1. Nadav Rappoport
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  2. Nathan Linial
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  3. Michal Linial
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Correspondence to Michal Linial.

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Competing interests

M.B., G-J.M. and S.v.D. are employed by Forbion Capital Partners.

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Supplementary Text, Supplementary Tables 1–9 and Supplementary Figures 1–3 (DOCX 1586 kb)

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Rappoport, N., Linial, N. & Linial, M. ProtoNet: charting the expanding universe of protein sequences. Nat Biotechnol 31, 290–292 (2013). https://doi.org/10.1038/nbt.2553

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