alexa Incorporating background frequency improves entropy-based residue conservation measures.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Data Mining in Genomics & Proteomics

Author(s): Wang K, Samudrala R

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Abstract BACKGROUND: 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. RESULTS: 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. CONCLUSION: Our results suggest that the application of appropriate background frequency information may lead to more biologically relevant results in many areas of bioinformatics.
This article was published in BMC Bioinformatics and referenced in Journal of Data Mining in Genomics & Proteomics

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