TRviz: a Python library for decomposing and visualizing tandem repeat sequences. [PDF]
Bioinform Adv, 2023 Summary TRviz is an open-source Python library for decomposing, encoding, aligning and visualizing tandem repeat (TR) sequences. TRviz takes a collection of alleles (TR containing sequences) and one or more motifs as input and generates a plot showing ...
Park J +3 more
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Typing
BMC Microbiology, 2009 Background Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies.
Harmanus Celine +6 more
doaj +6 more sources
PLoS Neglected Tropical Diseases, 2008 BackgroundInadequate understanding of the transmission of Mycobacterium leprae makes it difficult to predict the impact of leprosy control interventions. Genotypic tests that allow tracking of individual bacterial strains would strengthen epidemiological
Saroj K Young +7 more
doaj +3 more sources
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. [PDF]
Genome Res, 2022 Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans.
Gall-Duncan T +3 more
europepmc +2 more sources
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization. [PDF]
BMC Bioinformatics, 2017 Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases.
Nikumbh S, Pfeifer N.
europepmc +2 more sources
Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
Genome Biology, 2021 Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions.
Readman Chiu +3 more
doaj +2 more sources
Short Tandem Repeat-Enriched Architectural RNAs in Nuclear Bodies: Functions and Associated Diseases
Non-Coding RNA, 2020 Nuclear bodies are membraneless, phase-separated compartments that concentrate specific proteins and RNAs in the nucleus. They are believed to serve as sites for the modification, sequestration, and storage of specific factors, and to act as ...
Kensuke Ninomiya, Tetsuro Hirose
doaj +2 more sources
Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system [PDF]
BMC Microbiology, 2008 BackgroundSeveral methods have been reported for strain typing of Mycoplasma genitalium. The value of these methods has never been comparatively assessed.
Liang Ma +5 more
openalex +2 more sources
A comprehensive tandem repeat catalog of the human genome [PDF]
Nature CommunicationsWith the increasing availability of long-read sequencing data, high-quality human genome assemblies, and software for fully characterizing tandem repeats, genome-wide genotyping of tandem repeat loci on a population scale is becoming more feasible.
Readman Chiu +3 more
doaj +2 more sources
Diverse short tandem repeat sequences influence gene regulation in human populations [PDF]
Genome BiologyBackground Short tandem repeat (STR) length is a known determinant of pathogenicity in a variety of human disorders. The repeat sequence itself can modulate disease severity and penetrance; however, the broader impact of STR sequence variation on gene ...
Aleksandra Mitina +5 more
doaj +2 more sources