Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families.

ABSTRACT: The construction of a high-quality multiple sequence alignment (MSA) from copies of a transposable element (TE) is a critical step in the characterization of a new TE family. Most studies of MSA accuracy have been conducted on protein or RNA sequence families, where structural features and strong signals of selection may assist with alignment. Less attention has been given to the quality of sequence alignments involving neutrally evolving DNA sequences such as those resulting from TE replication. Transposable element sequences are challenging to align due to their wide divergence ranges, fragmentation, and predominantly-neutral mutation patterns. To gain insight into the effects of these properties on MSA accuracy, we developed a simulator of TE sequence evolution, and used it to generate

SUBMITTER: Hubley R 

PROVIDER: S-EPMC9112768 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature