ArticleBMC bioinformatics2021
IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features.International journal of molecular sciences · 2025Article
- hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing.Molecular cell · 2024Article
- Elevated incidence of somatic mutations at prevalent genetic sites.Briefings in bioinformatics · 2024Article
- Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals.Virus evolution · 2024Article
- Article
- Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae).BMC plant biology · 2023Article
- Nuclear and Mitochondrial Genome Assemblies of the Beetle, Zygogramma bicolorata, a Globally Important Biocontrol Agent of Invasive Weed Parthenium hysterophorus.Genome biology and evolution · 2023Article
- Pangenome-level analysis of nucleoid-associated proteins in theFrontiers in microbiology · 2023Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundAn inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets.
resultsWe present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats.
conclusionWithin the parameters that were tested, our experimental results show that IUPACPAL compares favourably to a similar application packaged with EMBOSS. We show that IUPACPAL identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.
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