ArticleBMC bioinformatics2019
GPRED-GC: a Gene PREDiction model accounting for 5
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.BMC genomics · 2025Article
- An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions.Bioinformatics advances · 2025Review
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Authors and funding
3 authors.
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Abstract
backgroundGene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tools and they have been widely used for gene annotation for various species. However, existing tools are not optimized for identifying genes with highly variable GC content. In addition, some genes in grass genomes exhibit a sharp 5
resultsIn this work, we designed and implemented a new hidden Markov model (HMM)-based ab initio gene prediction tool, which is optimized for finding genes with highly variable GC contents, such as the genes with negative GC gradients in grass genomes. We tested the tool on three datasets from Arabidopsis thaliana and Oryza sativa. The results showed that our tool can identify genes missed by existing tools due to the highly variable GC contents.
conclusionsGPRED-GC can effectively predict genes with highly variable GC contents without manual intervention. It provides a useful complementary tool to existing ones such as Augustus for more sensitive gene discovery. The source code is freely available at https://sourceforge.net/projects/gpred-gc/.
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