基本信息

Detecting pseudogene candidates from the annotated files of genomes

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Pseudogene is a non-functional DNA segment that resembles a functional gene, with most of them being redundant copies of functional genes. These copies are typically identified as pseudogenes due to the presence of frameshift mutations or premature stop codons. Although pseudogenes may contain promoter elements that potentially allow for low-level transcription and the subsequent production of RNA, they generally cannot be translated into functional protein products.

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Pseudofinder is a bioinformatics tool that detects pseudogene candidates from annotated genbank files of bacterial and archaeal genomes.

Pseudofinder uses a reference-based approach to detect a wide variety of pseudogene-inducing substitutions and gene structures, giving users many customizable options for defining pseudogenes. This software can use comparisons to large protein databases and/or closely related genomes to interrogate pseudogenes and selective pressures at the detailed gene-by-gene level.

补充信息

Related links:

https://github.com/filip-husnik/pseudofinder

参考文献

Syberg-Olsen MJ, Garber AI, Keeling PJ, McCutcheon JP, Husnik F. Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes. Mol Biol Evol. 2022;39(7):msac153. doi:10.1093/molbev/msac153