10779/rcsi.10782878.v1
Colm T. O'Dushlaine
Colm T.
O'Dushlaine
Denis C. Shields
Denis C.
Shields
Tools for the identification of variable and potentially variable tandem repeats.
Royal College of Surgeons in Ireland
2019
Algorithms
Databases
Genetic
Genome
Bacterial
Mycobacterium tuberculosis
Neisseria meningitidis
Reproducibility of Results
Software
Tandem Repeat Sequences
Clinical Pharmacology and Therapeutics
2019-11-22 16:21:23
Journal contribution
https://repository.rcsi.com/articles/journal_contribution/Tools_for_the_identification_of_variable_and_potentially_variable_tandem_repeats_/10782878
<p>BACKGROUND: Tandem repeat arrays showing variation between sequences within a population, between strains or across species may have functional effects. The increasing availability of genomic sequence data makes routine description of observed variation possible, creating a need for tools to describe such variability.</p>
<p>RESULTS: We present a set of programs that facilitate the identification of tandem repeats showing variation across multiple sequences or genomes, and the prediction of potentially polymorphic tandem repeats. The VNTRfinder (Variable Number of Tandem Repeats finder) program enables the detection of sequence length variation between arrays of inter-specific or intra-specific tandem repeats. In the absence of comparable sequences to explore observed variation, predictions are provided describing which tandem repeats are more likely to be variable, to help guide and focus further experimental evaluation.</p>
<p>CONCLUSION: These tools represent a resource for researchers interested in tandem repeats in nucleotide sequences that are most likely to be of clinical and evolutionary interest. The tools are available at http://bioinformatics.rcsi.ie/vntrfinder/. Downloadable versions for UNIX/LINUX and WINDOWS which permit the consideration of longer and more numerous sequences are also available.</p>