RT Journal
A1 Zhang, Yaran
A1 Hulsman, Marc
A1 Salazar, Alex
A1 Tesi, Niccolò
A1 Knoop, Lydian
A1 van der Lee, Sven
A1 Wijesekera, Sanduni
A1 Krizova, Jana
A1 Kamsteeg, Erik-Jan
A1 Holstege, Henne
T1 Multisample motif discovery and visualization for tandem repeats
JF Genome Research 
JO Genome Research 
YR 2025 
FD April 01 
VO 35 
IS 4 
SP 850 
OP 862 
DO 10.1101/gr.279278.124 
UL http://genome.cshlp.org/content/35/4/850.abstract 
AB Tandem repeats (TRs) occupy a significant portion of the human genome and are a source of polymorphisms due to variations in sizes and motif compositions. Some of these variations have been associated with various neuropathological disorders, highlighting the clinical importance of assessing the motif structure of TRs. Moreover, assessing the TR motif variation can offer valuable insights into evolutionary dynamics and population structure. Previously, characterizations of TRs were limited by short-read sequencing technology, which lacks the ability to accurately capture the full TR sequences. As long-read sequencing becomes more accessible and can capture the full complexity of TRs, there is now also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for the characterization and visualization of TRs based on a de novo k-mer approach for motif discovery. Comparative analysis against established tools reveals that MotifScope can identify a greater number of motifs and more accurately represent the underlying repeat sequences. Moreover, MotifScope has been specifically designed to enable motif composition comparisons across assemblies of different individuals, as well as across long-read sequencing reads within an individual, through combined motif discovery and sequence alignment. We showcase potential applications of MotifScope in diverse fields, including population genetics, clinical settings, and forensic analyses.