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FastAnnotator- an efficient transcript annotation web tool

机译：FastAnnotator-高效的成绩单标注网络工具

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Background Recent developments in high-throughput sequencing (HTS) technologies have made it feasible to sequence the complete transcriptomes of non-model organisms or metatranscriptomes from environmental samples. The challenge after generating hundreds of millions of sequences is to annotate these transcripts and classify the transcripts based on their putative functions. Because many biological scientists lack the knowledge to install Linux-based software packages or maintain databases used for transcript annotation, we developed an automatic annotation tool with an easy-to-use interface. Methods To elucidate the potential functions of gene transcripts, we integrated well-established annotation tools: Blast2GO, PRIAM and RPS BLAST in a web-based service, FastAnnotator, which can assign Gene Ontology (GO) terms, Enzyme Commission numbers (EC numbers) and functional domains to query sequences. Results Using six transcriptome sequence datasets as examples, we demonstrated the ability of FastAnnotator to assign functional annotations. FastAnnotator annotated 88.1% and 81.3% of the transcripts from the well-studied organisms Caenorhabditis elegans and Streptococcus parasanguinis , respectively. Furthermore, FastAnnotator annotated 62.9%, 20.4%, 53.1% and 42.0% of the sequences from the transcriptomes of sweet potato, clam, amoeba, and Trichomonas vaginalis , respectively, which lack reference genomes. We demonstrated that FastAnnotator can complete the annotation process in a reasonable amount of time and is suitable for the annotation of transcriptomes from model organisms or organisms for which annotated reference genomes are not avaiable. Conclusions The sequencing process no longer represents the bottleneck in the study of genomics, and automatic annotation tools have become invaluable as the annotation procedure has become the limiting step. We present FastAnnotator, which was an automated annotation web tool designed to efficiently annotate sequences with their gene functions, enzyme functions or domains. FastAnnotator is useful in transcriptome studies and especially for those focusing on non-model organisms or metatranscriptomes. FastAnnotator does not require local installation and is freely available at http://?fastannotator.?cgu.?edu.?tw .
机译：背景技术高通量测序（HTS）技术的最新发展使得对来自环境样品的非模式生物或元转录组的完整转录组进行测序成为可能。生成数亿个序列后的挑战是注释这些成绩单并根据其假定功能对成绩单进行分类。由于许多生物学家缺乏安装基于Linux的软件包或维护用于成绩单注释的数据库的知识，因此我们开发了具有易于使用的界面的自动注释工具。方法为了阐明基因转录本的潜在功能，我们在基于Web的服务FastAnnotator中集成了完善的注释工具：Blast2GO，PRIAM和RPS BLAST，可以分配基因本体论（GO）术语，酶委员会编号（EC编号）和功能域来查询序列。结果以六个转录组序列数据集为例，我们证明了FastAnnotator分配功能注释的能力。 FastAnnotator分别对来自经过充分研究的秀丽隐杆线虫和副链球菌的转录本分别进行了注释的88.1％和81.3％。此外，FastAnnotator分别注释了来自甘薯，蛤，变形虫和阴道毛滴虫的转录组的62.9％，20.4％，53.1％和42.0％的序列，这些序列缺少参考基因组。我们证明，FastAnnotator可以在合理的时间内完成注释过程，并且适合从模型生物或无法使用注释参考基因组的生物进行转录组注释。结论测序过程不再是基因组学研究的瓶颈，随着注释程序成为限制步骤，自动注释工具已变得无价之宝。我们介绍了FastAnnotator，这是一种自动注释网络工具，旨在有效注释具有基因功能，酶功能或结构域的序列。 FastAnnotator在转录组研究中非常有用，尤其是对于那些专注于非模式生物或元转录组的研究。 FastAnnotator不需要本地安装，可以从http：//？fastannotator。？cgu。？edu。？tw免费获得。

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