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Comparison of algorithms for prediction of related proteins using the method of phylogenetic profiles

  • Proteomics and Bioinformatics
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Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry Aims and scope Submit manuscript

Abstract

Computational interactomics deals with prediction of functionally related proteins. One approach for solving this problem using comparative genomics consists in analysis of similarities between phylogenetic profiles of proteins. In contrast to most methods, which predict only pairwise interactions between proteins, in the present work we have applied the cluster analysis techniques in order to find modules of functionally related proteins. We have performed the cluster analysis of phylogenetic profiles of E. coli proteins using several clustering techniques and various modes for estimation of distances between profiles. We report here, that the best correspondence in the composition of resultant clusters to known metabolic pathways is achieved using Ward’s clustering together with Hamming’s distance. The proposed technique of assessing predictions of the modules of functionally related proteins can be used for comparative analysis of different algorithms for computational interactomics.

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Authors and Affiliations

  1. Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, ul. Pogodinskaya 10, Moscow, 119121, Russia

    M. A. Pyatnitskiy, A. V. Lisitsa & A. I. Archakov

Authors
  1. M. A. Pyatnitskiy
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  2. A. V. Lisitsa
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  3. A. I. Archakov
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Correspondence to M. A. Pyatnitskiy.

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Original Russian Text © M.A. Pyatnitskiy, A.V. Lisitsa, A I. Archakov, 2010, published in Biomeditsinskaya Khimiya.

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Pyatnitskiy, M.A., Lisitsa, A.V. & Archakov, A.I. Comparison of algorithms for prediction of related proteins using the method of phylogenetic profiles. Biochem. Moscow Suppl. Ser. B 4, 42–48 (2010). https://doi.org/10.1134/S1990750810010063

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  • DOI: https://doi.org/10.1134/S1990750810010063

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