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Substitutional asymmetry programs

These programs test protein sequence data for substitutional asymmetry using the technique described in McDonald et al. (1999). Under the neutral model of protein evolution, a comparison of sequences from two species should show equal numbers of substitutions in each direction for each pair of amino acids. For example, when comparing the mesophile (moderate habitat temperature) Bacillus subtilis with the thermophile (high habitat temperature) Geobacillus stearothermophilus, you would expect the number of sites with alanine in B. subtilis and proline in G. stearothermophilus to equal the number of sites with proline in B. subtilis and alanine in G. stearothermophilus. In fact, a data set of 229 proteins showed 122 aligned sites with the first pattern and only 69 sites with the second pattern, suggesting that proline is preferred by natural selection over alanine in G. stearothermophilus (McDonald et al. 1999).

For some pairs of amino acids, substitutional asymmetry might be explained by differences in G+C content. For example, there are 412 lysine-->arginine substitutions between B. subtilis and G. stearothermophilus and only 157 arginine-->lysine substitutions. This may be explained by the higher G+C content of the G. stearothermophilus genome and the higher G+C content of arginine codons (AGR or CGN) over lysine (AAR). For inferring general patterns about which amino acids are favored in different environments, it is therefore preferable to compare species with similar genomic G+C contents, such as mesophilic Methanococcus spp. with the thermophile Methanocaldococus jannaschii (Haney et al. 1999, McDonald et al. 1999) or the moderate temperature (but radiation resistant!) Deinococcus radiodurans with the thermophile Thermus thermus (McDonald 2001).

Substitutional asymmetry is worth looking for in any comparison of related species that differ in some factor of the environment that might affect all proteins. Most examples of substitutional asymmetry come from comparisons of mesophiles and thermophiles (Haney et al. 1999, McDonald et al. 1999, McDonald 2001, Nishio et al. 2003), but substitutional asymmetry has also been found between the moderate-pressure Pyrococcus furiosus and the barophile P. abyssi (Di Giulio 2005).

The programs available here require a set of aligned homologous pairs of protein sequences from two species. The AmbiguityRemover program takes the file of sequences and puts ambiguously aligned sites next to alignment gaps in lower case, so they can be ignored by the AsymmetryCounter program. AsymmetryCounter counts the number of substitutions in each direction for each pair of amino acids, and compares the ratio to the expected 1:1 ratio using a test of goodness-of-fit. AsymmetryScaler finds an asymmetry index that illustrates how preferred or unpreferred each amino acid is in one species.

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