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公開日:2022/06/22 / 最終更新日:2022/06/22
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The relative mutability of amino acids in proteins has important implications for function. The significance of a particular amino acid is dependent on its position within the polypeptide. There is a large spectrum of patterns characterizing different amino acid subgroups. Specific patterns, so-called motifs or motif clusters, have recently been proposed. We identify sets of amino acid subgroups that display a common pattern, which we refer to as motif clusters, using a generalized multiple alignments approach to compute the distance between a pair of profiles and to cluster them, where profiles are sequences obtained by aligning all sequences in a multiple alignment. Motif clusters involve a relatively small number of different amino acid subgroups, each containing a distinct and conserved pattern. The method can be applied to any multiple alignment and is suitable for detecting motif clusters involving either conserved or non-conserved subgroups. We use our approach to re-analyse a set of protein multiple alignments and show that motif clusters can provide an important constraint on evolutionary models in comparative analyses.Does long-term treatment with nelfinavir reverse insulin resistance in patients with HIV-1 infection?
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