Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes.

ABSTRACT: Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder's multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typ

SUBMITTER: Syberg-Olsen MJ 

PROVIDER: S-EPMC9336565 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature