PseudoChecker: an integrated online platform for gene inactivation inference. Issue Volume 48:Issue W1(2020) (25th May 2020)

• Record Type: Journal Article
• Authors: Alves, Luís Q; Ruivo, Raquel; Fonseca, Miguel M; Lopes-Marques, Mónica; Ribeiro, Pedro; Castro, L Filipe C
• Is Part Of: Nucleic acids research. Volume 48:Issue W1(2020)
• Page Start: W321
• Page End: W331
• Publication Date: 2020-05-25
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa408
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: The rapid expansion of high-quality genome assemblies, exemplified by ongoing initiatives such as the Genome-10K and i5k, demands novel automated methods to approach comparative genomics. Of these, the study of inactivating mutations in the coding region of genes, or pseudogenization, as a source of evolutionary novelty is mostly overlooked. Thus, to address such evolutionary/genomic events, a systematic, accurate and computationally automated approach is required. Here, we present Pseudo Checker, the first integrated online platform for gene inactivation inference. Unlike the few existing methods, our comparative genomics-based approach displays full automation, a built-in graphical user interface and a novel index, PseudoIndex, for an empirical evaluation of the gene coding status. As a multi-platform online service, Pseudo Checker simplifies access and usability, allowing a fast identification of disruptive mutations. An analysis of 30 genes previously reported to be eroded in mammals, and 30 viable genes from the same lineages, demonstrated that Pseudo Checker was able to correctly infer 97% of loss events and 95% of functional genes, confirming its reliability. Pseudo Checker is freely available, without login required, at http://pseudochecker.ciimar.up.pt .