ArticleNucleic acids research2013
Graph-based modeling of tandem repeats improves global multiple sequence alignment.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 28 citations in OpenAlex.
- Distinct repeat architecture landscapes in the proteomes of protozoan parasites.NAR genomics and bioinformatics · 2026Article
- Insights into Mitochondrial Rearrangements and Selection in Accipitrid Mitogenomes, with New Data onGenes · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- The Dual Role of the Innate Immune System in the Effectiveness of mRNA Therapeutics.International journal of molecular sciences · 2023Review
- Ehrlichia SLiM ligand mimetic activates Hedgehog signaling to engage a BCL-2 anti-apoptotic cellular program.PLoS pathogens · 2022Article
- Article
- Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.Nucleic acids research · 2019Review
- Progressive multiple sequence alignment with indel evolution.BMC bioinformatics · 2018Article
- Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.Plant physiology · 2017Article
- Historian: accurate reconstruction of ancestral sequences and evolutionary rates.Bioinformatics (Oxford, England) · 2017Article
- Evolution of Protein Domain Repeats in Metazoa.Molecular biology and evolution · 2016Article
- Functional assignment to positively selected sites in the core type III effector RipG7 from Ralstonia solanacearum.Molecular plant pathology · 2016Article
- DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment.BMC bioinformatics · 2015Article
- Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions.Molecular biology and evolution · 2015Article
- A depauperate immune repertoire precedes evolution of sociality in bees.Genome biology · 2015Article
- Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences.Molecular biology and evolution · 2015Article
- Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.Frontiers in bioengineering and biotechnology · 2015Review
- QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically.Frontiers in plant science · 2015Article
- Deep conservation of human protein tandem repeats within the eukaryotes.Molecular biology and evolution · 2014Article
- Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex.BMC genomics · 2013Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.