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PseudoChecker: an integrated online platform for gene inactivation inference
PseudoChecker: an integrated online platform for gene inactivation inference
- 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.
- Subjects :
- 0106 biological sciences
AcademicSubjects/SCI00010
Pseudogene
Inference
Genomics
Computational biology
Biology
010603 evolutionary biology
01 natural sciences
Genome
03 medical and health sciences
Genetics
Animals
Coding region
Codon
030304 developmental biology
Comparative genomics
0303 health sciences
business.industry
Usability
Identification (information)
Mutation
Web Server Issue
business
Sequence Alignment
Pseudogenes
Software
Subjects
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