Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China.
Nucleic Acids Res. 2023 Jul 5;51(W1):W17-W24. doi: 10.1093/nar/gkad400.
The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http://cao.labshare.cn/abalign/.
高通量测序（HTS）在适应性免疫和抗体药物开发领域中被广泛应用于 B 细胞受体（BCR）免疫受体谱分析。然而，这些实验产生的大量序列给数据处理带来了挑战。具体来说，BCR 分析的关键方面——多重序列比对（MSA），对于处理海量 BCR 测序数据仍然不够充分，并且缺乏提供免疫球蛋白特异性信息的能力。为了解决这一差距，我们引入了 Abalign，这是一个专门为 BCR/抗体序列的超快 MSA 设计的独立程序。基准测试表明，Ablalign 达到了与最先进的 MSA 工具相当甚至更好的准确性，并且在速度和内存消耗方面具有显著优势，将高通量分析所需的时间从数周缩短到数小时。除了其对齐功能外，Ablalign 还提供了广泛的 BCR 分析功能，包括提取 BCR、构建谱系树、分配 VJ 基因、分析克隆型、分析突变和比较 BCR 免疫受体谱。Ablalign 具有用户友好的图形界面，可以在个人计算机上轻松运行，而无需使用计算集群。总的来说，Ablalign 是一个易于使用且有效的工具，使研究人员能够分析海量的 BCR/抗体序列，从而在免疫信息学领域取得新的发现。该软件可在 http://cao.labshare.cn/abalign/ 免费获取。
