Van Bel Michiel, Proost Sebastian, Van Neste Christophe, Deforce Dieter, Van de Peer Yves, Vandepoele Klaas
Genome Biol. 2013 Dec 13;14(12):R134. doi: 10.1186/gb-2013-14-12-r134.
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/.
通过新一代测序技术进行转录组分析，可以为非模式物种生成详细的基因目录，但代价是在计算需求和生物信息学专业知识方面面临新的挑战。在此，我们展示了TRAPID，这是一个用于快速高效处理组装好的RNA-Seq转录组数据的在线工具，其开发目的是缓解这些挑战。TRAPID提供高通量开放阅读框检测、移码校正，并包括一个功能、比较和系统发育工具箱，利用了175个参考蛋白质组。与最先进的转录本分析工具进行基准测试和比较，揭示了TRAPID系统的效率和独特功能。TRAPID可在http://bioinformatics.psb.ugent.be/webtools/trapid/免费获取。
