Blanco Celia, Tee Allison, Sharma Pramesh, Newton Matilda S, Lee Kun-Hwa, Erickson Samuel E, Seelig Burckhard, Chen Irene A
Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA, USA.
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA.
J Mol Evol. 2025 Apr;93(2):229-237. doi: 10.1007/s00239-025-10244-w. Epub 2025 Apr 5.
In vitro evolution is a powerful technique for identifying functional nucleic acids and peptides, but the analysis of the resulting high-throughput sequencing data poses significant challenges, particularly in peptide selections. Existing bioinformatics tools often lack the specificity needed for this task, leaving researchers to navigate complex datasets with inadequate resources. To address these challenges, we present EasyDIVER + , an enhanced pipeline building on the foundation of the original EasyDIVER tool, which was designed for pre-processing sequencing data. EasyDIVER + not only processes raw, paired-end, demultiplexed Illumina read files but also introduces advanced analytical capabilities, including the calculation of enrichment values for each unique sequence across consecutive selection rounds. Furthermore, EasyDIVER + offers a highly flexible and customizable visualization platform, enabling detailed graphical representations of sequence metrics. These new features mark a significant advance in bioinformatics for peptide and protein data, providing researchers with intuitive tools for comprehensive data analysis and interpretation.
体外进化是一种用于鉴定功能性核酸和肽的强大技术，但对由此产生的高通量测序数据进行分析面临重大挑战，尤其是在肽的筛选方面。现有的生物信息学工具往往缺乏完成这项任务所需的特异性，使得研究人员在资源不足的情况下处理复杂的数据集。为应对这些挑战，我们推出了EasyDIVER +，这是一个在原始EasyDIVER工具基础上构建的增强型流程，该工具专为预处理测序数据而设计。EasyDIVER +不仅能处理原始的、双端的、已解复用的Illumina读取文件，还引入了先进的分析功能，包括计算连续选择轮次中每个独特序列的富集值。此外，EasyDIVER +提供了一个高度灵活且可定制的可视化平台，能够生成序列指标的详细图形表示。这些新功能标志着肽和蛋白质数据生物信息学的重大进展，为研究人员提供了用于全面数据分析和解释的直观工具。
