Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2013 Dec 13;14(12):R134.
doi: 10.1186/gb-2013-14-12-r134.

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Michiel Van Bel, Sebastian Proost, Christophe Van Neste, Dieter Deforce, Yves Van de Peer, Klaas Vandepoele
Comparative Study

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Michiel Van Bel et al. Genome Biol. .

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/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Schematic overview of the TRAPID pipeline. The TRAPID pipeline consists of two separate steps. The first one is a non-interactive processing step, during which all transcripts are assigned to gene families using a RAPSearch2 similarity search, followed by functional annotation transfer and meta-annotation assignment. The second step is interactive and directly commanded through the website interface. Here, the user has the ability to analyze his data using functional enrichment analyses, multiple sequence alignments, and phylogenetic trees.
Figure 2
Figure 2
Visualization of a phylogenetic tree with associated meta-annotation labels per transcript. Cladogram based on a FastTree2 phylogenetic tree for the alpha/beta-Hydrolases superfamily (based on PLAZA 2.5 gene family HOM002165). Transcripts are marked in black, while colored gene identifiers refer to homologs from reference species: Ostreococcus tauri (ota), Physcomitrella patens (ppa), Populus trichocarpa (ptr), Arabidopsis thaliana (ath), Oryza sativa ssp. Japonica (osa), Sorghum bicolor (sbo), and Zea mays (zma). Meta-annotation for the different transcripts is visualized using the colored boxes on the right.
See this image and copyright information in PMC

References

    1. Kodama Y, Shumway M, Leinonen R. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 2012;14:D54–D56. doi: 10.1093/nar/gkr854. - DOI - PMC - PubMed
    1. Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011;14:469–477. doi: 10.1038/nmeth.1613. - DOI - PubMed
    1. Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet. 2011;14:671–682. doi: 10.1038/nrg3068. - DOI - PubMed
    1. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;14:1966–1967. doi: 10.1093/bioinformatics/btp336. - DOI - PubMed
    1. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nat Methods. 2010;14:909–912. doi: 10.1038/nmeth.1517. - DOI - PubMed

Publication types

MeSH terms