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

Authors
  • Alamro, Hayam1, 2
  • Alzamel, Mai1, 3
  • Iliopoulos, Costas S.1
  • Pissis, Solon P.4, 5
  • Watts, Steven1
  • 1 King’s College London, 30 Aldwych, London, UK , London (United Kingdom)
  • 2 Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia , Riyadh (Saudi Arabia)
  • 3 King Saud University, Riyadh, Kingdom of Saudi Arabia , Riyadh (Saudi Arabia)
  • 4 Centrum Wiskunde & Informatica, Amsterdam, The Netherlands , Amsterdam (Netherlands)
  • 5 Vrije Universiteit Amsterdam, Amsterdam, The Netherlands , Amsterdam (Netherlands)
Type
Published Article
Journal
BMC Bioinformatics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Feb 06, 2021
Volume
22
Issue
1
Identifiers
DOI: 10.1186/s12859-021-03983-2
Source
Springer Nature
Keywords
License
Green

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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