Krait2: a versatile software for microsatellite investigation, visualization and marker development
Abstract 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...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11252-2 |
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| author | Lianming Du Jiahao Chen Dalin Sun Kelei Zhao Qianglin Zeng Nan Yang |
| author_facet | Lianming Du Jiahao Chen Dalin Sun Kelei Zhao Qianglin Zeng Nan Yang |
| author_sort | Lianming Du |
| collection | DOAJ |
| description | Abstract 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 . |
| format | Article |
| id | doaj-art-262cbb42f9a3461797259d01e3b19372 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-262cbb42f9a3461797259d01e3b193722025-01-26T12:16:43ZengBMCBMC Genomics1471-21642025-01-012611710.1186/s12864-025-11252-2Krait2: a versatile software for microsatellite investigation, visualization and marker developmentLianming Du0Jiahao Chen1Dalin Sun2Kelei Zhao3Qianglin Zeng4Nan Yang5Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu UniversityAntibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu UniversityAntibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu UniversityAntibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu UniversityAntibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu UniversityKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu UniversityAbstract 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 .https://doi.org/10.1186/s12864-025-11252-2MicrosatelliteTandem repeatsGenomesGenetic markerPrimer design |
| spellingShingle | Lianming Du Jiahao Chen Dalin Sun Kelei Zhao Qianglin Zeng Nan Yang Krait2: a versatile software for microsatellite investigation, visualization and marker development BMC Genomics Microsatellite Tandem repeats Genomes Genetic marker Primer design |
| title | Krait2: a versatile software for microsatellite investigation, visualization and marker development |
| title_full | Krait2: a versatile software for microsatellite investigation, visualization and marker development |
| title_fullStr | Krait2: a versatile software for microsatellite investigation, visualization and marker development |
| title_full_unstemmed | Krait2: a versatile software for microsatellite investigation, visualization and marker development |
| title_short | Krait2: a versatile software for microsatellite investigation, visualization and marker development |
| title_sort | krait2 a versatile software for microsatellite investigation visualization and marker development |
| topic | Microsatellite Tandem repeats Genomes Genetic marker Primer design |
| url | https://doi.org/10.1186/s12864-025-11252-2 |
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