Bridging the gaps in statistical models of protein alignment.

ABSTRACT:

Summary

Sequences of proteins evolve by accumulating substitutions together with insertions and deletions (indels) of amino acids. However, it remains a common practice to disconnect substitutions and indels, and infer approximate models for each of them separately, to quantify sequence relationships. Although this approach brings with it computational convenience (which remains its primary motivation), there is a dearth of attempts to unify and model them systematically and together. To overcome this gap, this article demonstrates how a complete statistical model quantifying the evolution of pairs of aligned proteins can be constructed using a time-parameterized substitution matrix and a time-parameterized alignment state machine. Methods to derive all parameters of such a model f

SUBMITTER: Sumanaweera D 

PROVIDER: S-EPMC9235498 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature