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Open Access Open Badges Methodology article

Incorporating background frequency improves entropy-based residue conservation measures

Kai Wang and Ram Samudrala*

Author Affiliations

Computational Genomics Group, Department of Microbiology, University of Washington, USA

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BMC Bioinformatics 2006, 7:385  doi:10.1186/1471-2105-7-385

Published: 17 August 2006



Several entropy-based methods have been developed for scoring sequence conservation in protein multiple sequence alignments. High scoring amino acid positions may correlate with structurally or functionally important residues. However, amino acid background frequencies are usually not taken into account in these entropy-based scoring schemes.


We demonstrate that using a relative entropy measure that incorporates amino acid background frequency results in improved performance in identifying functional sites from protein multiple sequence alignments.


Our results suggest that the application of appropriate background frequency information may lead to more biologically relevant results in many areas of bioinformatics.