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Background <p>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.</p> Results <p>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.</p> Conclusions <p>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 <a href="https://github.com/lmdu/krait2">https://github.com/lmdu/krait2</a>.</p>

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Krait2: a versatile software for microsatellite investigation, visualization and marker development

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年1月25日

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  • Lianming Du,
  • Jiahao Chen,
  • Dalin Sun,
  • Kelei Zhao,
  • Qianglin Zeng,
  • Nan Yang

摘要

Background

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.

Results

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.

Conclusions

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.