ArticleBioinformatics (Oxford, England)2017
Kmer-SSR: a fast and exhaustive SSR search algorithm.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Development of strain specific simple sequence repeats and assessment of genetic diversity in Erwinia amylovora from marker selection to phylogenetic analysis.Scientific reports · 2025Article
- Pytrf: a python package for finding tandem repeats from genomic sequences.BMC bioinformatics · 2025Article
- Gene conversion and duplication contribute to genetic variation in an outbreak ofMicrobial genomics · 2025Article
- The first engkabang jantong (Data in brief · 2025Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- 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
- MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data.Frontiers in big data · 2021Article
- SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects.Applications in plant sciences · 2020Article
- SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences.Frontiers in genetics · 2020Article
- Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19.Informatics in medicine unlocked · 2020Article
- IDSSR: An Efficient Pipeline for Identifying Polymorphic Microsatellites from a Single Genome Sequence.International journal of molecular sciences · 2019Article
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3 authors.
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Abstract
motivationOne of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a 'good enough' solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a 'good enough' solution may not accurately portray results in population genetics, phylogenetics and forensics, which require accurate SSRs to calculate intra- and inter-species interactions.
resultsWe present Kmer-SSR, which finds all SSRs faster than most heuristic SSR identification algorithms in a parallelized, easy-to-use manner. The exhaustive Kmer-SSR option has 100% precision and 100% recall and accurately identifies every SSR of any specified length. To identify more biologically pertinent SSRs, we also developed several filters that allow users to easily view a subset of SSRs based on user input. Kmer-SSR, coupled with the filter options, accurately and intuitively identifies SSRs quickly and in a more user-friendly manner than any other SSR identification algorithm. AVAILABILITY AND IMPLEMENTATION: The source code is freely available on GitHub at https://github.com/ridgelab/Kmer-SSR. CONTACT: perry.ridge@byu.edu.
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