ArticleNucleic acids research2020
PseudoChecker: an integrated online platform for gene inactivation inference.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Parallel Erosion of a Testis-Specific Na+/K+ ATPase in Three Mammalian Lineages Sheds Light into the Evolution of Spermatozoa Energetics.Genome biology and evolution · 2026Article
- Deciphering genetic adaptations of Old World camels through comparative genomic analyses across all camelid species.iScience · 2025Article
- Gene Loss DB: a curated database for gene loss in mammals-the cetacean collection.Database : the journal of biological databases and curation · 2025Article
- PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era.Bioinformatics advances · 2025Article
- Article
- Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes.Molecular biology and evolution · 2022Article
- Functional or Vestigial? The Genomics of the Pineal Gland in Xenarthra.Journal of molecular evolution · 2021Article
- Convergent Loss of the Necroptosis Pathway in Disparate Mammalian Lineages Shapes Viruses Countermeasures.Frontiers in immunology · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.