Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy.

ABSTRACT: Ancestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a phylogeny describing the history of the protein family and a model of the molecular-evolutionary process to infer the sequences of ancient proteins, allowing researchers to directly investigate the impact of sequence evolution on protein structure and function. Like all statistical inferences, ASR can be sensitive to violations of its underlying assumptions. Previous studies have shown that, whereas phylogenetic uncertainty has only a very weak impact on ASR accuracy, uncertainty in the protein sequence alignment can more strongly affect inferred ancestral sequences. Here, we show that errors in sequence alignment can produce errors in ASR across a range of realistic and simplified evolutionary scenari

SUBMITTER: Aadland K 

PROVIDER: S-EPMC7523730 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature