ArticleScientific reports2017
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- 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
- Differential Gene Expression Correlates with Behavioural Polymorphism during Collective Behaviour in Cockroaches.Animals : an open access journal from MDPI · 2022Article
- RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative.Frontiers in genetics · 2022Article
- Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).PloS one · 2021Article
- Wood transcriptome analysis and expression variation of lignin biosynthetic pathway transcripts inJournal of biosciences · 2021Article
- Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding.Scientific reports · 2020Article
- Molecular basis of resistance to organophosphate insecticides in the New World screw-worm fly.Parasites & vectors · 2020Article
- Data on theData in brief · 2020Article
- Contribution of introns to the species diversity associated with the apicomplexan parasite, Neospora caninum.Parasitology research · 2020Article
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- Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants.Bioinformatics (Oxford, England) · 2019Article
- De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway.Scientific reports · 2019Article
- Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods.BMC genomics · 2019Article
- The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome.Frontiers in genetics · 2019Article
- In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.Scientific reports · 2018Article
- Draft genome sequence ofData in brief · 2018Article
- Deep sequencing analysis of toadThe journal of venomous animals and toxins including tropical diseases · 2018Article
- A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant-Microbe Interactions.Frontiers in plant science · 2018Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
absatractAlong with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization. To accelerate the annotation process, we have optimized the computation processes and used parallel computing for all annotation steps. Moreover, FunctionAnnotator is designed to be versatile, and it generates a variety of useful outputs for facilitating other analyses. Here, we demonstrate how FunctionAnnotator can be helpful in annotating non-model organisms. We further illustrate that FunctionAnnotator can estimate the taxonomic composition of environmental samples and assist in the identification of novel proteins by combining RNA-Seq data with proteomics technology. In summary, FunctionAnnotator can efficiently annotate transcriptomes and greatly benefits studies focusing on non-model organisms or metatranscriptomes. FunctionAnnotator, a comprehensive annotation web-service tool, is freely available online at: http://fa.cgu.edu.tw/ . This new web-based annotator will shed light on field studies involving organisms without a reference genome.
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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.