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Splitting the BLOSUM Score into Numbers of Biological Significance

EURASIP Journal on Bioinformatics and Systems Biology20072007:31450

Received: 2 October 2006

Accepted: 30 March 2007

Published: 4 June 2007


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.


Protein SequenceBiological SignificanceFrequency DivergenceProtein ModelMathematical Tool


Authors’ Affiliations

Dipartimento di Matematica e Informatica, Università degli Studi di Trieste, Trieste, Italy
Centro di Biomedicina Molecolare, AREA Science Park, Basovizza, Italy
Dipartimento di Biochimica, Biofisica, e Chimica delle Macromolecole, Università degli Studi di Trieste, Trieste, Italy


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© Francesco Fabris et al. 2007

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