ArticleGenome research2006
Iterative gene prediction and pseudogene removal improves genome annotation.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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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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Who cites it
30 citing papers in PubMed, 75 citations in OpenAlex.
- PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era.Bioinformatics advances · 2025Article
- Genomic evidence of contemporary hybridization between Schistosoma species.PLoS pathogens · 2022Article
- Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes.Molecular biology and evolution · 2022Article
- PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data.BMC bioinformatics · 2022Article
- Genome annotation of disease-causing microorganisms.Briefings in bioinformatics · 2021Review
- Computational Methods for Pseudogene Annotation Based on Sequence Homology.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing.Biology · 2020Review
- PseudoChecker: an integrated online platform for gene inactivation inference.Nucleic acids research · 2020Article
- Overcoming challenges and dogmas to understand the functions of pseudogenes.Nature reviews. Genetics · 2020Review
- Article
- Origination and Function of Plant Pseudogenes.Plant signaling & behavior · 2019Article
- The CaspBase: a curated database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference.Protein science : a publication of the Protein Society · 2018Article
- Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes.Scientific reports · 2017Article
- Review
- Pseudogenes and Their Genome-Wide Prediction in Plants.International journal of molecular sciences · 2016Review
- Article
- Finding protein-coding genes through human polymorphisms.PloS one · 2013Article
- DNA-energetics-based analyses suggest additional genes in prokaryotes.Journal of biosciences · 2012Article
- TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.Frontiers in plant science · 2012Article
- Approaches to Fungal Genome Annotation.Mycology · 2011Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Correct gene prediction is impaired by the presence of processed pseudogenes: nonfunctional, intronless copies of real genes found elsewhere in the genome. Gene prediction programs frequently mistake processed pseudogenes for real genes or exons, leading to biologically irrelevant gene predictions. While methods exist to identify processed pseudogenes in genomes, no attempt has been made to integrate pseudogene removal with gene prediction, or even to provide a freestanding tool that identifies such erroneous gene predictions. We have created PPFINDER (for Processed Pseudogene finder), a program that integrates several methods of processed pseudogene finding in mammalian gene annotations. We used PPFINDER to remove pseudogenes from N-SCAN gene predictions, and show that gene prediction improves substantially when gene prediction and pseudogene masking are interleaved. In addition, we used PPFINDER with gene predictions as a parent database, eliminating the need for libraries of known genes. This allows us to run the gene prediction/PPFINDER procedure on newly sequenced genomes for which few genes are known.
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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.