ArticleGenes2021
Detection of Highly Divergent Tandem Repeats in the Rice Genome.
Article in Genes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Both semi-dwarf and photoperiod-insensitive traits in rice were important for the Green Revolution.Botanical studies · 2026Article
- 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
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- Detection of tandem repeats in the Capsicum annuum genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Article
- Use of 6 Nucleotide Length Words to Study the Complexity of Gene Sequences from Different Organisms.Entropy (Basel, Switzerland) · 2022Article
- Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences.International journal of molecular sciences · 2022Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, there is a lack of bioinformatics approaches to identify highly divergent tandem repeats (TRs) in eukaryotic genomes. Here, we developed a new mathematical method to search for TRs, which uses a novel algorithm for constructing multiple alignments based on the generation of random position weight matrices (RPWMs), and applied it to detect TRs of 2 to 50 nucleotides long in the rice genome. The RPWM method could find highly divergent TRs in the presence of insertions or deletions. Comparison of the RPWM algorithm with the other methods of TR identification showed that RPWM could detect TRs in which the average number of base substitutions per nucleotide (x) was between 1.5 and 3.2, whereas T-REKS and TRF methods could not detect divergent TRs with x > 1.5. Applied to the search of TRs in the rice genome, the RPWM method revealed that TRs occupied 5% of the genome and that most of them were 2 and 3 bases long. Using RPWM, we also revealed the correlation of TRs with dispersed repeats and transposons, suggesting that some transposons originated from TRs. Thus, the novel RPWM algorithm is an effective tool to search for highly divergent TRs in the genomes.
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Registered trials
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