TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes
Open Access
- 1 January 2013
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 14 (12), R134
- https://doi.org/10.1186/gb-2013-14-12-r134
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 systemThis publication has 34 references indexed in Scilit:
- Oases:robustde novoRNA-seq assembly across the dynamic range of expression levelsBioinformatics, 2012
- Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel researchThe Plant Journal, 2012
- The Transcriptome Analysis and Comparison Explorer—T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organismsBioinformatics, 2012
- Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative studyBMC Bioinformatics, 2011
- Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtlesEvoDevo, 2011
- Computational methods for transcriptome annotation and quantification using RNA-seqNature Methods, 2011
- De novo assembly and analysis of RNA-seq dataNature Methods, 2010
- SOAP2: an improved ultrafast tool for short read alignmentBioinformatics, 2009
- Jalview Version 2—a multiple sequence alignment editor and analysis workbenchBioinformatics, 2009
- prot4EST: Translating Expressed Sequence Tags from neglected genomesBMC Bioinformatics, 2004