ArticleNucleic acids research2011
A new repeat-masking method enables specific detection of homologous sequences.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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135 citing papers in PubMed.
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- De novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing.The Journal of heredity · 2026Article
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- Mitotic microhomology-mediated break-induced replication promotes chromoanasynthesis.Nature communications · 2026Article
- Finding low-complexity DNA sequences with longdust.Bioinformatics (Oxford, England) · 2026Article
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- Stable genome structures in living fossil fishes.Genome research · 2026Article
- The role of low-complexity repeats in RNA-RNA interactions and a deep learning framework for duplex prediction.Nature communications · 2026Article
- Genomic and physiological signatures of adaptation in pathogenic fungi.Nature communications · 2026Article
- Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition.Bioinformatics advances · 2026Article
- Genome sequence of the novel Cystobasidiomycetes fungal isolate EMM_F5.Microbiology resource announcements · 2025Article
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- First genome sequences of the dinoflagellate Effrenium voratum strain isolated from the coral Hydnophora exesa in temperate Japanese region.BMC genomic data · 2025Article
- Telomeric assemblies ofbioRxiv : the preprint server for biology · 2025Article
- GPU-accelerated homology search with MMseqs2.Nature methods · 2025Article
- Discovery of additional ancient genome duplications in yeasts.bioRxiv : the preprint server for biology · 2025Article
75 more citing papers are in PubMed but not listed here.
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1 author.
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No grant is acknowledged in the PubMed record.
Abstract
Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, TANTAN, which is motivated by the mechanisms that create simple repeats. This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.
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