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 +8 more sources
APE1 incision activity at abasic sites in tandem repeat sequences. [PDF]
J Mol Biol, 2014 Repetitive DNA sequences, such as are present in micro- and mini-satellites, telomeres, and trinucleotide repeats (linked to fragile X syndrome, Huntington disease, etc.), account for nearly 30% of the human genome.
Li M +3 more
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Repeat or not repeat?—Statistical validation of tandem repeat prediction in genomic sequences [PDF]
Nucleic Acids Research, 2012 Tandem repeats (TRs) represent one of the most prevalent features of genomic sequences. Due to their abundance and functional significance, a plethora of detection tools has been devised over the last two decades.
Elke Schaper +2 more
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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 +2 more
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Use of short tandem repeat sequences to study Mycobacterium leprae in leprosy patients in Malawi and India. [PDF]
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
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Tandem repeat sequences evolutionarily related to SVA-type retrotransposons are expanded in the centromere region of the western hoolock gibbon, a small ape [PDF]
Journal of Human Genetics, 2012 Hoolock hoolock (the western hoolock gibbon) is a species of the family Hylobatidae (small apes), which constitutes the superfamily Hominoidea (hominoids) together with Hominidae (great apes and human).
Yuriko Hirai +2 more
exaly +3 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
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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.
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