PseudoChecker: an integrated online platform for gene inactivation inference

• Type: Article in International Scientific Journal
• Date: 2020

Authors

Alves, LQ (Author) Other; Ruivo, R (Author) Other; Fonseca, MM (Author) Other; Lopes Marques, M (Author) Other; Pedro Ribeiro (Author) FCUP; Filipe F C Castro (Author) FCUP

Journal

Title: Nucleic Acids Research

Vol. 48

Pages: W321-W331

ISSN: 0305-1048

Publisher: Oxford University Press

Indexing

ISI Web of Knowledge - 0 Citations

Scopus - 8 Citations

Other information

Authenticus ID: P-00S-5AY

DOI: 10.1093/nar/gkaa408

Abstract (EN): 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 PseudoChecker, 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, PseudoChecker 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 PseudoChecker was able to correctly infer 97% of loss events and 95% of functional genes, confirming its reliability. PseudoChecker is freely available, without login required, at http://pseudochecker.ciimar.up.pt.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 11