ArticleBioinformatics (Oxford, England)2014
A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it, 16 citations in OpenAlex.
- 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
- LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes.Nucleic acids research · 2022Article
- IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences.BMC bioinformatics · 2021Article
- 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
- detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes.Scientific reports · 2016Article
- detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.PloS one · 2014Article
- The combined use of antimullerian hormone and age to predict the ovarian response to controlled ovarian hyperstimulation in poor responders: A novel approach.Journal of human reproductive sciences · 2013Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
summaryPalindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA-protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs. AVAILABILITY AND IMPLEMENTATION: The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php) CONTACT: liangc@miamioh.edu or karroje@miamioh.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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What OpenQuestion holds
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.