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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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present<jats:sc>IUPACpal<\/jats:sc>, 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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Within the parameters that were tested, our experimental results show that<jats:sc>IUPACpal<\/jats:sc>compares favourably to a similar application packaged with<jats:sc>EMBOSS<\/jats:sc>. We show that<jats:sc>IUPACpal<\/jats:sc>identifies many previously unidentified inverted repeats when compared with<jats:sc>EMBOSS<\/jats:sc>, and that\u00a0this is also performed with orders of magnitude improved speed.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-021-03983-2","type":"journal-article","created":{"date-parts":[[2021,2,8]],"date-time":"2021-02-08T18:42:00Z","timestamp":1612809720000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences"],"prefix":"10.1186","volume":"22","author":[{"given":"Hayam","family":"Alamro","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mai","family":"Alzamel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Costas S.","family":"Iliopoulos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1445-1932","authenticated-orcid":false,"given":"Solon P.","family":"Pissis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven","family":"Watts","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,2,6]]},"reference":[{"key":"3983_CR1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-84800-255-5","volume-title":"Computing for comparative microbial genomics: bioinformatics for microbiologists","author":"DW Ussery","year":"2009","unstructured":"Ussery DW, Wassenaar TM, Borini S. 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