ArticleBMC bioinformatics2013
MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Progresses of transposon research inSynthetic and systems biotechnology · 2026Review
- Review
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Identification and Characterization ofGenes · 2022Article
- Methodologies for theGenes · 2022Review
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A sensitive repeat identification framework based on short and long reads.Nucleic acids research · 2021Article
- Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome.BMC plant biology · 2021Article
- Genome sequence and evolution of Betula platyphylla.Horticulture research · 2021Article
- Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding.Molecular biology reports · 2020Review
- Characterization of B-Genome Specific High Copy hAT MITE Families inFrontiers in plant science · 2020Article
- Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies.Scientific reports · 2019Article
- Amplification of miniature inverted-repeat transposable elements and the associated impact on gene regulation and alternative splicing in mulberry (Mobile DNA · 2019Article
- MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies.Mobile DNA · 2019Article
- MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes.BMC medical genomics · 2018Article
- MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes.BMC bioinformatics · 2018Article
- Article
- MUSTv2: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs).Journal of integrative bioinformatics · 2017Article
- Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions.Scientific reports · 2017Article
- Article
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Abstract
backgroundMiniature inverted repeat transposable elements (MITEs) are abundant non-autonomous elements, playing important roles in shaping gene and genome evolution. Their characteristic structural features are suitable for automated identification by computational approaches, however, de novo MITE discovery at genomic levels is still resource expensive. Efficient and accurate computational tools are desirable. Existing algorithms process every member of a MITE family, therefore a major portion of the computing task is redundant.
resultsIn this study, redundant computing steps were analyzed and a novel algorithm emphasizing on the reduction of such redundant computing was implemented in MITE Digger. It completed processing the whole rice genome sequence database in ~15 hours and produced 332 MITE candidates with low false positive (1.8%) and false negative (0.9%) rates. MITE Digger was also tested for genome wide MITE discovery with four other genomes.
conclusionsMITE Digger is efficient and accurate for genome wide retrieval of MITEs. Its user friendly interface further facilitates genome wide analyses of MITEs on a routine basis. The MITE Digger program is available at: http://labs.csb.utoronto.ca/yang/MITEDigger.
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