Faculty of Computer Engineering, Federal University of Pará campus Tucuruí (CAMTUC-UFPA), Pará, Brazil.
Federal Institute of Pará, IFPA, Pará, Brazil.
Gene. 2022 Nov 30;844:146819. doi: 10.1016/j.gene.2022.146819. Epub 2022 Aug 25.
The reduction in the cost of DNA sequencing and the total time to perform this process has resulted in a significant increase in the deposit of biological information in public databases such as the NCBI (National Center for Biotechnology Information). The production of large volumes of data per run has culminated in the need to develop algorithms capable of handling data with this new feature and assisting in analyses such as the assembly and annotation of prokaryotic genomes. Over the years, several pipelines and computational tools have been developed to automate this task and consequently reduce the total time to know the genetic content of a given organism, especially non-model organisms, collaborating with the identification of possible targets with biotechnological applicability. In the case of automatic annotation tools, the accuracy of the results is widely observed in the literature, however, this does not excludes the manual curation process, where the information inferred in the automatic process is verified and enriched by the curators. This task requires a time which is directly proportional to the number of gene products of the target organism under study. To assist in this process, we present the ReNoteWeb web tool, endowed with a simple and intuitive interface, to perform the assembly enhancement process, with the possibility of identifying the missing products in the original genomic sequence. In addition, ReNoteWeb is capable of performing the annotation process for all products, based on information obtained from highly accurate external databases. The engine responsible for performing the data processing was developed in JAVA and the web platform uses the resources of the Yii framework. The annotation produced by this platform aims to reduce the overall time in the manual curation process. Twenty-three organisms were used to validate the tool. The efficiency was verified by comparing the annotation of these same organisms available in the NCBI database and the annotation performed on the RAST platform. The tool is available at: http://biod.ufpa.br/renoteweb/.
DNA 测序成本的降低和完成该过程的总时间的减少，导致生物信息在公共数据库（如 NCBI（国家生物技术信息中心））中的存储显著增加。每次运行产生的大量数据，最终需要开发能够处理具有此新特征的数据的算法，并协助进行分析，如原核基因组的组装和注释。多年来，已经开发了几个管道和计算工具来自动化这项任务，从而减少了解给定生物体（特别是非模式生物体）的遗传内容的总时间，同时有助于识别具有生物技术应用可能性的可能目标。在自动注释工具的情况下，文献中广泛观察到结果的准确性，但是，这并不能排除手动编辑过程，其中在自动过程中推断的信息由编辑者验证和丰富。这项任务需要的时间与正在研究的目标生物体的基因产物数量成正比。为了帮助完成此过程，我们提供了 ReNoteWeb 网络工具，它具有简单直观的界面，用于执行组装增强过程，并有可能识别原始基因组序列中缺失的产物。此外，ReNoteWeb 能够根据从高度准确的外部数据库获得的信息，对所有产物执行注释过程。负责执行数据处理的引擎是用 JAVA 开发的，网络平台利用 Yii 框架的资源。该平台产生的注释旨在减少手动编辑过程的总时间。使用了二十三个生物体来验证该工具。通过比较 NCBI 数据库中这些相同生物体的注释和 RAST 平台上执行的注释，验证了该工具的效率。该工具可在以下网址获得：http://biod.ufpa.br/renoteweb/。
