ArticleBMC bioinformatics2013
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Next-Generation Whole-Exome Pattern: Advanced Methods and Clinical Significance.Current gene therapy · 2026Review
- InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data.Nucleic acids research · 2020Article
- The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates.Journal of visualized experiments : JoVE · 2018Article
- T-REx: Transcriptome analysis webserver for RNA-seq Expression data.BMC genomics · 2015Article
- NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome.BMC plant biology · 2015Article
- Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome).RNA biology · 2015Article
- RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.BMC genomics · 2015Article
- A platform independent RNA-Seq protocol for the detection of transcriptome complexity.BMC genomics · 2013Article
- Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics skills and computational resources well beyond the possibilities of many "wet biology" laboratories. Moreover, most of projects only require few sequencing cycles and standard tools or workflows to carry out suitable analyses for the identification and annotation of genes, transcripts and splice variants found in the biological samples under investigation. These projects can take benefits from the availability of easy to use systems to automatically analyse sequences and to mine data without the preventive need of strong bioinformatics background and hardware infrastructure.
resultsTo address this issue we developed an automatic system targeted to the analysis of NGS data obtained from large-scale transcriptome studies. This system, we named NGS-Trex (NGS Transcriptome profile explorer) is available through a simple web interface http://www.ngs-trex.org and allows the user to upload raw sequences and easily obtain an accurate characterization of the transcriptome profile after the setting of few parameters required to tune the analysis procedure. The system is also able to assess differential expression at both gene and transcript level (i.e. splicing isoforms) by comparing the expression profile of different samples.By using simple query forms the user can obtain list of genes, transcripts, splice sites ranked and filtered according to several criteria. Data can be viewed as tables, text files or through a simple genome browser which helps the visual inspection of the data.
conclusionsNGS-Trex is a simple tool for RNA-Seq data analysis mainly targeted to "wet biology" researchers with limited bioinformatics skills. It offers simple data mining tools to explore transcriptome profiles of samples investigated taking advantage of NGS technologies.
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