ArticleBMC bioinformatics2007
Detecting microsatellites within genomes: significant variation among algorithms.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- High-fidelity, large-scale targeted profiling of microsatellites.Genome research · 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
- Detection of tandem repeats in the Capsicum annuum genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison.Frontiers in genetics · 2023Article
- Complete Chloroplast Genome ofPlants (Basel, Switzerland) · 2020Article
- Complete Chloroplast Genome Characterization ofPlants (Basel, Switzerland) · 2020Article
- Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer.Nucleic acids research · 2019Article
- Invasions of gladiolus rust in North America are caused by a widely-distributed clone ofPeerJ · 2019Article
- A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies.Frontiers in genetics · 2018Article
- Molecular and Computational Methods for the Detection of Microsatellite Instability in Cancer.Frontiers in oncology · 2018Review
- Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species.PloS one · 2018Article
- In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis.Database : the journal of biological databases and curation · 2017Article
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.BMC bioinformatics · 2015Article
- Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.Frontiers in bioengineering and biotechnology · 2015Review
- Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species.SpringerPlus · 2015Article
- Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution.PloS one · 2015Article
- ProGeRF: proteome and genome repeat finder utilizing a fast parallel hash function.BioMed research international · 2015Article
- Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs.Plant molecular biology · 2014Article
- The landscape of human STR variation.Genome research · 2014Article
Corrections and comments
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundMicrosatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker).
resultsOur analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster) spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp), regardless of motif.
conclusionSince the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.
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