ArticleGenome biology2013
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed, 135 citations in OpenAlex.
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- Multi-omic analysis tools for microbial metabolites prediction.Briefings in bioinformatics · 2024Review
- Histologic, metabolomic, and transcriptomic differences in fir trees from a peri-urban forest under chronic ozone exposure.Ecology and evolution · 2024Article
- Integrated mRNA and small RNA sequencing reveals post-transcriptional regulation of the sesquiterpene pathway in3 Biotech · 2023Article
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- A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane.Plant communications · 2023Article
- Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism.Scientific reports · 2022Article
- A simple guide to de novo transcriptome assembly and annotation.Briefings in bioinformatics · 2022Review
- De novo transcriptome assembly and identification of G-Protein-Coupled-Receptors (GPCRs) in two species of monogenean parasites of fish.Parasite (Paris, France) · 2022Article
- Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco.Science advances · 2021Article
- TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.Nucleic acids research · 2021Article
- De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism.BMC genomics · 2021Article
- Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate.The ISME journal · 2021Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/.
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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.