ArticleBioinformatics (Oxford, England)2019
Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It has been retracted, and should not be counted. Cited by 12 papers.
What it found
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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.
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
12 citing papers in PubMed.
- Hayai-Annotation: A functional gene prediction tool that integrates orthologs and gene ontology for network analysis in plant species.Computational and structural biotechnology journal · 2025Article
- Chromosome-level genome assembly of Solanum pimpinellifolium.Scientific data · 2024Article
- Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species.BMC plant biology · 2023Article
- Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in the genus Eustoma.G3 (Bethesda, Md.) · 2023Article
- Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- An improved reference genome forFrontiers in plant science · 2023Article
- A de novo genome assembly of Solanum verrucosum Schlechtendal, a Mexican diploid species geographically isolated from other diploid A-genome species of potato relatives.G3 (Bethesda, Md.) · 2022Article
- De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza.The New phytologist · 2022Article
- Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato.Scientific reports · 2020Article
- Oxford Nanopore sequencing: new opportunities for plant genomics?Journal of experimental botany · 2020Article
- Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis).DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
Corrections and comments
- Retraction · 2023-07-01Error in Analyses · Error in Data · Unreliable Results and/or Conclusions · · see also: https://academic.oup.com/bioinformatics/article/36/22-23/5558/6042706;
- Commented on by
- Retracted
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryHayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate functional gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: i) protein name; ii) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function and Cellular Component); iii) enzyme commission number; iv) protein existence level; and v) evidence type. It implements a new algorithm that gives priority to protein existence level to propagate GO and EC information and annotated Arabidopsis thaliana representative peptide sequences (Araport11) within 5 min at the PC level. AVAILABILITY AND IMPLEMENTATION: The software is implemented in R and runs on Macintosh and Linux systems. It is freely available at https://github.com/kdri-genomics/Hayai-Annotation-Plants under the GPLv3 license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.