BibTeX
@MISC{07,
author = {},
title = {},
year = {2007}
}
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Abstract
Capra et al We consider six previously introduced methods for estimating the conservation of a column within an MSA. The first and most commonly used method estimates conservation by calculating the Shannon entropy of the amino acid distribution of each column (Durbin et al., 1998). The second attempts to take amino acid similarity into account by partitioning the amino acids into stereochemically similar groups and then calculating the Shannon entropy in terms of this partition (Williamson, 1995; Mirny and Shakhnovich, 1999). The third incorporates the similarities between amino acids by adapting the von Neumann entropy to operate on an substitution matrix (Caffrey et al., 2004). The fourth calculates the relative entropy (Cover and Thomas, 1991) between a column distribution and a background distribution (Wang and Samudrala, 2006); it is similar to our measure in that it attempts to identify sites that have amino
