ArticleGenome research2009
Evidence-based gene predictions in plant genomes.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 59 citations in OpenAlex.
- Cookbook for plant genome sequences.BMC genomics · 2026Review
- Improved reconstruction of transcripts and coding sequences from RNA-seq data.Nucleic acids research · 2026Article
- Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq.Genome research · 2025Article
- Proteogenomic Gene Structure Validation in the Pineapple Genome.Journal of proteome research · 2024Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice.Science China. Life sciences · 2021Article
- Gene Validation and Remodelling Using Proteogenomics ofFrontiers in microbiology · 2021Article
- Genome structure and evolution of Antirrhinum majus L.Nature plants · 2019Article
- Evidence-based gene models for structural and functional annotations of the oil palm genome.Biology direct · 2017Article
- Sequencing and de novo assembly of a near complete indica rice genome.Nature communications · 2017Article
- Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.Nature communications · 2016Article
- Using intron position conservation for homology-based gene prediction.Nucleic acids research · 2016Article
- Dual use of peptide mass spectra: Protein atlas and genome annotation.Current plant biology · 2015Article
- Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants.BMC plant biology · 2015Article
- Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.Plant physiology · 2015Article
- Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment.BMC bioinformatics · 2014Article
- ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity.BMC genomics · 2013Article
- Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum.PloS one · 2013Article
- Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.Nature communications · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Automated evidence-based gene building is a rapid and cost-effective way to provide reliable gene annotations on newly sequenced genomes. One of the limitations of evidence-based gene builders, however, is their requirement for transcriptional evidence-known proteins, full-length cDNAs, or expressed sequence tags (ESTs)-in the species of interest. This limitation is of particular concern for plant genomes, where the rate of genome sequencing is greatly outpacing the rate of EST- and cDNA-sequencing projects. To overcome this limitation, we have developed an evidence-based gene build system (the Gramene pipeline) that can use transcriptional evidence across related species. The Gramene pipeline uses the Ensembl computing infrastructure with a novel data processing scheme. Using the previously annotated plant genomes, the dicot Arabidopsis thaliana and the monocot Oryza sativa, we show that the cross-species ESTs from within monocot or dicot class are a valuable source of evidence for gene predictions. We also find that, using only EST and cross-species evidence, the Gramene pipeline can generate a plant gene set that is comparable in quality to the human genes based on known proteins and full-length cDNAs. We compare the Gramene pipeline to several widely used ab initio gene prediction programs in rice; this comparison shows the pipeline performs favorably at both the gene and exon levels with cross-species gene products only. We discuss the results of testing the pipeline on a 22-Mb region of the newly sequenced maize genome and discuss potential application of the pipeline to other genomes.
Indexed as
Identifiers
What OpenQuestion holds
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.