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Splitting the BLOSUM Score into Numbers of Biological Significance

EURASIP Journal on Bioinformatics and Systems Biology volume 2007, Article number: 31450 (2007) Cite this article

Abstract

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.

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Authors and Affiliations

  1. Dipartimento di Matematica e Informatica, Università degli Studi di Trieste, via Valerio 12b, Trieste, 34127, Italy

    Francesco Fabris & Andrea Sgarro

  2. Centro di Biomedicina Molecolare, AREA Science Park, Strada Statale 14, Basovizza, Trieste, 34012, Italy

    Francesco Fabris & Andrea Sgarro

  3. Dipartimento di Biochimica, Biofisica, e Chimica delle Macromolecole, Università degli Studi di Trieste, via Licio Giorgieri 1, Trieste, 34127, Italy

    Alessandro Tossi

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  1. Francesco Fabris
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  2. Andrea Sgarro
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  3. Alessandro Tossi
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Correspondence to Francesco Fabris.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fabris, F., Sgarro, A. & Tossi, A. Splitting the BLOSUM Score into Numbers of Biological Significance. J Bioinform Sys Biology 2007, 31450 (2007). https://doi.org/10.1155/2007/31450

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