ArticlePloS one2014
detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops.Briefings in bioinformatics · 2022Pooled it
- Short Inverted Repeats as Mutational Hotspots and Putative Drivers of Genome Instability in Osteosarcoma.Genes · 2025Article
- invertiaDB: a database of inverted repeats across organismal genomes.Nucleic acids research · 2025Article
- invertiaDB: A Database of Inverted Repeats Across Organismal Genomes.bioRxiv : the preprint server for biology · 2024Article
- CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs.Scientific reports · 2024Article
- Detection of alternative DNA structures and its implications for human disease.Molecular cell · 2023Review
- Dynamic alternative DNA structures in biology and disease.Nature reviews. Genetics · 2023Review
- LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes.Nucleic acids research · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus.BMC genomics · 2021Article
- Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.MicrobiologyOpen · 2020Article
- Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection.Plant physiology · 2019Article
- PCIR: a database of Plant Chloroplast Inverted Repeats.Database : the journal of biological databases and curation · 2019Article
- MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes.BMC medical genomics · 2018Article
- Lirex: A Package for Identification of Long Inverted Repeats in Genomes.Genomics, proteomics & bioinformatics · 2017Article
- detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes.Scientific reports · 2016Article
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Authors and funding
4 authors.
Funding
Abstract
Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.
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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.