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PseudoChecker: an integrated online platform for gene inactivation inference

PseudoChecker: an integrated online platform for gene inactivation inference

Authors :
Mónica Lopes-Marques
Raquel Ruivo
Miguel Fonseca
L. Filipe C. Castro
Luís Q. Alves
Pedro Ribeiro
Source :
Nucleic Acids Research
Publication Year :
2020
Publisher :
Oxford University Press (OUP), 2020.

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 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.

Details

ISSN :
13624962 and 03051048
Volume :
48
Database :
OpenAIRE
Journal :
Nucleic Acids Research
Accession number :
edsair.doi.dedup.....5f699da7cf5adfbaca5b7a078f0c9608
Full Text :
https://doi.org/10.1093/nar/gkaa408