ArticleEvolutionary bioinformatics online2008
Detecting microsatellites in genome data: variance in definitions and bioinformatic approaches cause systematic bias.
Article in Evolutionary bioinformatics online, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context.Molecular genetics and genomics : MGG · 2026Article
- Evaluation of genetic diversity and structure of the endangered medicinal plant genusPhytoKeys · 2026Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- VarSCAT: A computational tool for sequence context annotations of genomic variants.PLoS computational biology · 2023Article
- PhasomeIt: an 'omics' approach to cataloguing the potential breadth of phase variation in the genus Campylobacter.Microbial genomics · 2018Article
- Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.Frontiers in bioengineering and biotechnology · 2015Review
- Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution.PloS one · 2015Article
- Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species.PloS one · 2012Article
- Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs).Parasites & vectors · 2011Article
- A monte carlo method for assessing the quality of duplication-aware alignment algorithms.Evolutionary bioinformatics online · 2011Article
- Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.BMC genomics · 2010Article
- Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness.BMC genomics · 2010Article
- Article
- What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats.Genome biology and evolution · 2010Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Microsatellites are currently one of the most commonly used genetic markers. The application of bioinformatic tools has become common practice in the study of these short tandem repeats (STR). However, in silico studies can suffer from study bias. Using a meta-analysis on microsatellite distribution in yeast we show that estimates of numbers of repeats reported by different studies can differ in the order of several magnitudes, even within a single genome. These differences arise because varying definitions of microsatellites, spanning repeat size, array length and array composition, are used in different search paradigms, with minimum array length being the main influencing factor. Structural differences in the implemented search algorithm additionally contribute to variation in the number of repeats detected. We suggest that for future studies a consistent approach to STR searches is adopted in order to improve the power of intra- and interspecific comparisons.
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