Research output: Contribution to journal › Article › peer-review
Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts
Original language | English |
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Article number | 51 |
Journal | BMC Bioinformatics |
Volume | 22 |
Issue number | 1 |
Early online date | Feb 2021 |
DOIs | |
Accepted/In press | 27 Jan 2021 |
E-pub ahead of print | Feb 2021 |
Published | 6 Feb 2021 |
Additional links |
IUPACpal efcient identifcation_ALAMRO_Acc27Jan2021Epub6Feb_GOLD VoR(CC BY)
IUPACpal_efcient_identifcation_ALAMRO_Acc27Jan2021Epub6Feb_GOLD_VoR_CC_BY_.pdf, 2.15 MB, application/pdf
Uploaded date:08 Jun 2021
Version:Final published version
Licence:CC BY
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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