DOI: 10.1073/pnas.96.8.4285. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

10.1073/pnas.96.8.4285

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

Determining protein functions from genomic sequences is a central goal of bioinformatics. We present a method based on the assumption that proteins that function together in a pathway or structural complex are likely to evolve in a correlated fashion. During evolution, all such functionally linked proteins tend to be either preserved or eliminated in a new species. We describe this property of correlated evolution by characterizing each protein by its phylogenetic profile, a string that encodes the presence or absence of a protein in every known genome. We show that proteins having matching or similar profiles strongly tend to be functionally linked. This method of phylogenetic profiling allows us to predict the function of uncharacterized proteins.

Bibliography

Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., & Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proceedings of the National Academy of Sciences, 96(8), 4285â4288.

Authors 5

Matteo Pellegrini (first)
Edward M. Marcotte (additional)
Michael J. Thompson (additional)
David Eisenberg (additional)
Todd O. Yeates (additional)

References 9 Referenced 1,404

Dates

Type	When
Created	23 years ago (July 26, 2002, 10:39 a.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 5:16 p.m.)
Indexed	2 weeks, 2 days ago (Aug. 6, 2025, 8:47 a.m.)
Issued	26 years, 4 months ago (April 13, 1999)
Published	26 years, 4 months ago (April 13, 1999)
Published Online	26 years, 4 months ago (April 13, 1999)
Published Print	26 years, 4 months ago (April 13, 1999)

Funders 0

None

BibTeX

@article{Pellegrini_1999, title={Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles}, volume={96}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.96.8.4285}, DOI={10.1073/pnas.96.8.4285}, number={8}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Pellegrini, Matteo and Marcotte, Edward M. and Thompson, Michael J. and Eisenberg, David and Yeates, Todd O.}, year={1999}, month=apr, pages={4285–4288} }

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