PseudoChecker: an integrated online platform for gene inactivation inference.

Nucleic Acids Res

CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal.

Published: July 2020

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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319564PMC
http://dx.doi.org/10.1093/nar/gkaa408DOI Listing

Publication Analysis

Top Keywords

pseudochecker integrated
8
integrated online
8
online platform
8
platform gene
8
pseudochecker
4
gene inactivation
4
inactivation inference
4
inference rapid
4
rapid expansion
4
expansion high-quality
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!