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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)
78 Downloads (Pure)

Abstract

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.

Original languageEnglish
Article number51
JournalBMC Bioinformatics
Volume22
Issue number1
Early online dateFeb 2021
DOIs
Publication statusPublished - 6 Feb 2021

Keywords

  • Gaps
  • Inverted repeat
  • IUPAC
  • Mismatches
  • Palindrome
  • Software

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