ArticleFrontiers in plant science2012
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.
Article in Frontiers in plant science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 76 citations in OpenAlex.
- Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes.NAR genomics and bioinformatics · 2026Article
- Progress and innovations of gene cloning in wheat and its close relatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- A survey of lineage-specific genes inPlant direct · 2023Article
- Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding.GigaScience · 2022Article
- The complete genome sequence of elite bread wheat cultivar, "Sonmez".F1000Research · 2022Article
- OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security.Plants (Basel, Switzerland) · 2021Review
- The wheat Seven in absentia gene is associated with increases in biomass and yield in hot climates.Journal of experimental botany · 2021Article
- A Major Locus on Wheat Chromosome 7B Associated With Late-Maturity α-Amylase Encodes a PutativeFrontiers in plant science · 2021Article
- Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency.Plant physiology · 2020Article
- Rapid evolution of α-gliadin gene family revealed by analyzing Gli-2 locus regions of wild emmer wheat.Functional & integrative genomics · 2019Article
- Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long-Read Technologies.The plant genome · 2019Article
- Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize.PloS one · 2019Article
- Genome-wide identification and analysis of non-specific Lipid Transfer Proteins in hexaploid wheat.Scientific reports · 2018Article
- Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat.Scientific reports · 2018Article
- Gene Duplication and Evolution Dynamics in the Homeologous Regions Harboring Multiple Prolamin and Resistance Gene Families in Hexaploid Wheat.Frontiers in plant science · 2018Article
- Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order.BMC genomics · 2017Article
- Mapping stripe rust resistance gene YrZH22 in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- A TRIM insertion in the promoter of Ms2 causes male sterility in wheat.Nature communications · 2017Article
- Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight.Nature genetics · 2016Article
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Authors and funding
24 authors at 6 institutions in 8 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future.
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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.