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

BMC Bioinformatics

Solon P. Pissis¹  Costas S. Iliopoulos²  Steven Watts²  Mai Alzamel³  Hayam Alamro⁴ 

[1] Centrum Wiskunde & Informatica, Amsterdam, The Netherlands;Vrije Universiteit Amsterdam, Amsterdam, The Netherlands;Department of Informatics, King’s College London, 30 Aldwych, London, UK;Department of Informatics, King’s College London, 30 Aldwych, London, UK;Computer Science Department, King Saud University, Riyadh, Kingdom of Saudi Arabia;Department of Informatics, King’s College London, 30 Aldwych, London, UK;Department of Information Systems, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia;

关键词: Inverted repeat;    Palindrome;    Gaps;    Mismatches;    Software;    IUPAC;   

DOI  :  10.1186/s12859-021-03983-2

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY