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. 2007 Jun 4;2007(1):31450. doi: 10.1155/2007/31450

Splitting the BLOSUM Score into Numbers of Biological Significance

Francesco Fabris 1,2,✉, Andrea Sgarro 1,2, Alessandro Tossi 3
PMCID: PMC3171334  PMID: 18369412

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.

[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]

Contributor Information

Francesco Fabris, Email: frnzfbrs@dmi.units.it.

Andrea Sgarro, Email: sgarro@units.it.

Alessandro Tossi, Email: tossi@bbcm.units.it.

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