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IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences

Research output: Contribution to journalArticlepeer-review

Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts

Original languageEnglish
Article number51
JournalBMC Bioinformatics
Issue number1
Early online dateFeb 2021
Accepted/In press27 Jan 2021
E-pub ahead of printFeb 2021
Published6 Feb 2021

Bibliographical note

Funding Information: This project was supported by EPSRC DTA grant EP/M50788X-1. The funding body did not influence the study, collection, analysis or interpretation of any data. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 872539. Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.


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Background: An 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. Results: We 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. Conclusion: Within 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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