Biotechvana, Parc Científic Universitat de València, Valencia, Spain.
Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
Bioinformatics. 2021 Jul 12;37(11):1610-1612. doi: 10.1093/bioinformatics/btaa903.
Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis.
SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets.
SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual.
Supplementary data are available at Bioinformatics online.
为了研究蛋白质和 DNA/RNA 序列的特定特征、模式和功能，通常需要基于图形界面的工具，这些工具的主要特点是直观，并且与用户的专业知识具有交互性，尤其是在需要进行注释或引物设计任务时。然而，基于界面的工具在处理大型序列或复杂数据集（如基因组和转录组组装）时通常会受到某些计算限制。考虑到这些要求，我们开发了 SeqEditor，这是一种用于核苷酸和蛋白质序列分析的交互式软件工具。
SeqEditor 是一个用于核苷酸和蛋白质序列分析的跨平台桌面应用程序。它通过图形用户界面进行管理，可以作为图形序列浏览器使用，也可以作为多 FASTA 文件的快速 FASTA 任务管理器使用。SeqEditor 经过优化，可以处理大型序列，如连续体、支架，甚至染色体，并包括一个 GTF/GFF 查看器，用于可视化和管理注释文件。反过来，这使得从参考基因组和转录组中进行内容挖掘的效率与命令行工具相似。SeqEditor 还包含一组用于单重和多重 PCR 引物设计和池化的工具，该工具使用了一种新的优化和验证的搜索策略，用于目标和物种特异性引物。所有这些功能使 SeqEditor 成为一种灵活的应用程序，可用于分析复杂序列、设计 PCR 检测中的引物，以及管理、编辑和个性化参考序列数据集。
SeqEditor 是使用 Java 语言在 Eclipse Rich Client Platform 上开发的，并在 https://gpro.biotechvana.com/download/SeqEditor 上以 Windows、Linux 和 Mac OS 的二进制文件形式提供。用户手册和教程可在 https://gpro.biotechvana.com/tool/seqeditor/manual 在线获取。
补充数据可在 Bioinformatics 在线获取。
