ArticleFrontiers in genetics2020
SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 27 citations in OpenAlex.
- Article
- A comprehensive full-length transcriptome atlas across multiple organs of an Indian yak breed-Arunachali.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- SSR_VibraProfiler: a Python package for accurate classification of varieties using SSRs with intra-variety specificity and inter-variety polymorphism.Plant methods · 2025Article
- Assembly and comparative analysis of the mitochondrial genome ofFrontiers in plant science · 2025Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- PPGV: a comprehensive database of peach population genome variation.BMC plant biology · 2024Article
- What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools.Frontiers in genetics · 2024Review
- Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding.BMC genomic data · 2023Article
- Genome assembly of the Korean intertidal mud-creeper Batillaria attramentaria.Scientific data · 2023Article
- TeaPVs: a comprehensive genomic variation database for tea plant (Camellia sinensis).BMC plant biology · 2022Article
- Fine mapping of the tiller inhibition gene TIN4 contributing to ideal plant architecture in common wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Frontiers in genetics · 2022Article
- The Insights into Mitochondrial Genomes of Sunflowers.Plants (Basel, Switzerland) · 2021Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microsatellites or simple sequence repeats (SSRs) are short tandem repeats of DNA widespread in genomes and transcriptomes of diverse organisms and are used in various genetic studies. Few software programs that mine SSRs can be further used to mine polymorphic SSRs, and these programs have poor portability, have slow computational speed, are highly dependent on other programs, and have low marker development rates. In this study, we develop an algorithm named Simple Sequence Repeat Molecular Marker Developer (SSRMMD), which uses improved regular expressions to rapidly and exhaustively mine perfect SSR loci from any size of assembled sequence. To mine polymorphic SSRs, SSRMMD uses a novel three-stage method to assess the conservativeness of SSR flanking sequences and then uses the sliding window method to fragment each assembled sequence to assess its uniqueness. Furthermore, molecular biology assays support the polymorphic SSRs identified by SSRMMD. SSRMMD is implemented using the Perl programming language and can be downloaded from https://github.com/GouXiangJian/SSRMMD.
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