Du Lianming, Chen Jiahao, Sun Dalin, Zhao Kelei, Zeng Qianglin, Yang Nan
Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610225, China.
BMC Genomics. 2025 Jan 25;26(1):72. doi: 10.1186/s12864-025-11252-2.
Microsatellites are highly polymorphic repeat sequences ubiquitously interspersed throughout almost all genomes which are widely used as powerful molecular markers in diverse fields. Microsatellite expansions play pivotal roles in gene expression regulation and are implicated in various neurological diseases and cancers. Although much effort has been devoted to developing efficient tools for microsatellite identification, there is still a lack of a powerful tool for large-scale microsatellite analysis.
We present Krait2, a user-friendly graphical tool for investigating perfect, imperfect and compound microsatellites from FASTA and FASTQ formatted genomic datasets. Krait2 not only provides features such as primer design, repeat filtering, repeat annotation and statistical analysis, but also offers various output formats to support customized downstream analysis. Moreover, it has capability of analyzing multiple genomes simultaneously and conducting comparative analysis.
Krait2 is a versatile and easy-to-use software for both novices and experts to identify and analyze microsatellites. The installer and source code are available at https://github.com/lmdu/krait2 .
微卫星是高度多态的重复序列，几乎普遍散布于所有基因组中，在不同领域被广泛用作强大的分子标记。微卫星扩展在基因表达调控中起关键作用，并与各种神经疾病和癌症有关。尽管已投入大量精力开发用于微卫星鉴定的高效工具，但仍缺乏用于大规模微卫星分析的强大工具。
我们展示了Krait2，这是一个用户友好的图形工具，用于从FASTA和FASTQ格式的基因组数据集中研究完美、不完美和复合微卫星。Krait2不仅提供引物设计、重复序列过滤、重复序列注释和统计分析等功能，还提供各种输出格式以支持定制的下游分析。此外，它能够同时分析多个基因组并进行比较分析。
Krait2是一款通用且易于使用的软件，新手和专家都可以用它来识别和分析微卫星。安装程序和源代码可在https://github.com/lmdu/krait2获取。
