ArticleBMC bioinformatics2014
Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements.
Article in BMC bioinformatics, 2014. 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.
- A high-throughput search for intracellular factors that affect RNA folding identifiesRNA biology · 2024Article
- Transposable element finder (TEF): finding active transposable elements from next generation sequencing data.BMC bioinformatics · 2022Article
- Genome ARTIST_v2-An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes.International journal of molecular sciences · 2022Article
- Experimentally heat-induced transposition increases drought tolerance in Arabidopsis thaliana.The New phytologist · 2022Article
- Tracing Mobile DNAs: From Molecular to Population Scales.Frontiers in plant science · 2022Review
- InMut-finder: a software tool for insertion identification in mutagenesis using Nanopore long reads.BMC genomics · 2021Article
- TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis.mBio · 2021Article
- Genomic impact of stress-induced transposable element mobility in Arabidopsis.Nucleic acids research · 2021Article
- Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare.G3 (Bethesda, Md.) · 2021Article
- Detection of Transposition Events from Next-Generation Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling.Nucleic acids research · 2019Article
- Article
- TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data.Microbial genomics · 2018Article
- TranSurVeyor: an improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data.Nucleic acids research · 2018Article
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- The Role of Transposable Elements in Speciation.Genes · 2018Review
- McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.G3 (Bethesda, Md.) · 2017Article
- Genomic analysis ofPeerJ · 2017Article
- DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.Genome research · 2016Article
- Quantitative assessment of insertion sequence impact on bacterial genome architecture.Microbial genomics · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS. We have developed a program with a new algorithm to detect the transpositions from NGS data.
resultsIn the process of tool development, we used next-generation sequence (NGS) data of derivative lines (ttm2 and ttm5) of japonica rice cv. Nipponbare, regenerated through cell culture. The new program, called a transposon insertion finder (TIF), was applied to detect the de novo transpositions of Tos17 in the regenerated lines. TIF searched 300 million reads of a line within 20 min, identifying 4 and 12 de novo transposition in ttm2 and ttm5 lines, respectively. All of the transpositions were confirmed by PCR/electrophoresis and sequencing. Using the program, we also detected new transposon insertions of P-element from NGS data of Drosophila melanogaster.
conclusionTIF operates to find the transposition of any elements provided that target site duplications (TSDs) are generated by their transpositions.
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Registered trials
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.