PseudoChecker: an integrated online platform for gene inactivation inference

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.

Figure 1.

Conceptualization of the three-step-based PseudoChecker’s computational pipeline.

Figure 2.

Typical output of a PseudoChecker analysis. General information related to the executed analysis is shown at the top. Below, the alignment executed by MACSE, detected gene inactivating mutations per full coding sequence and PseudoIndex value assigned for each target species corresponding sequence are presented. At the upper right corner, both ‘Export’ and ‘Display’ buttons are available for additional options.