ArticlePloS one2015
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Genetic marker: a genome mapping tool to decode genetic diversity of livestock animals.Frontiers in genetics · 2024Review
- A Guide to Conquer the Biological Network Era Using Graph Theory.Frontiers in bioengineering and biotechnology · 2020Review
- Ensemble of rankers for efficient gene signature extraction in smoke exposure classification.BMC bioinformatics · 2018Article
- An integrated approach to infer cross-talks between intracellular protein transport and signaling pathways.BMC bioinformatics · 2018Article
- Workflow and web application for annotating NCBI BioProject transcriptome data.Database : the journal of biological databases and curation · 2017Article
- An Atlas of annotations of Hydra vulgaris transcriptome.BMC bioinformatics · 2016Article
- A web-oriented software for the optimization of pooled experiments in NGS for detection of rare mutations.BMC research notes · 2016Article
- Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling.BMC bioinformatics · 2016Article
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Authors and funding
4 authors.
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Abstract
RNA-seq is a new tool to measure RNA transcript counts, using high-throughput sequencing at an extraordinary accuracy. It provides quantitative means to explore the transcriptome of an organism of interest. However, interpreting this extremely large data into biological knowledge is a problem, and biologist-friendly tools are lacking. In our lab, we developed Transcriptator, a web application based on a computational Python pipeline with a user-friendly Java interface. This pipeline uses the web services available for BLAST (Basis Local Search Alignment Tool), QuickGO and DAVID (Database for Annotation, Visualization and Integrated Discovery) tools. It offers a report on statistical analysis of functional and Gene Ontology (GO) annotation's enrichment. It helps users to identify enriched biological themes, particularly GO terms, pathways, domains, gene/proteins features and protein-protein interactions related informations. It clusters the transcripts based on functional annotations and generates a tabular report for functional and gene ontology annotations for each submitted transcript to the web server. The implementation of QuickGo web-services in our pipeline enable the users to carry out GO-Slim analysis, whereas the integration of PORTRAIT (Prediction of transcriptomic non coding RNA (ncRNA) by ab initio methods) helps to identify the non coding RNAs and their regulatory role in transcriptome. In summary, Transcriptator is a useful software for both NGS and array data. It helps the users to characterize the de-novo assembled reads, obtained from NGS experiments for non-referenced organisms, while it also performs the functional enrichment analysis of differentially expressed transcripts/genes for both RNA-seq and micro-array experiments. It generates easy to read tables and interactive charts for better understanding of the data. The pipeline is modular in nature, and provides an opportunity to add new plugins in the future. Web application is freely available at: http://www-labgtp.na.icar.cnr.it/Transcriptator.
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Registered trials
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