Bio-Protocol, 2022 Repeat expansion diseases, including fragile X syndrome, Huntington’s disease, and C9orf72-related motor neuron disease and frontotemporal dementia, are a group of disorders associated with polymorphic expansions of tandem repeat nucleotide sequences ...
Joanne Sharpe, Nikki Harper, Ryan West
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Linked-read sequencing for detecting short tandem repeat expansions
Scientific Reports, 2022 AbstractDetection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences. In this study, we explored how the long-range sequence information of barcode linked-read sequencing (BLRS) can be leveraged to improve repeat-read detection.
Readman Chiu +3 more
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Finding the region of pseudo-periodic tandem repeats in biological sequences [PDF]
Algorithms for Molecular Biology, 2006 The genomes of many species are dominated by short sequences repeated consecutively. It is estimated that over 10% of the human genome consists of tandemly repeated sequences. Finding repeated regions in long sequences is important in sequence analysis.
Xiaowen Liu, Lusheng Wang 0001
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Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat
Frontiers in Plant Science, 2015 The kinetochore is a protein complex including kinetochore-specific proteins that plays a role in chromatid segregation during mitosis and meiosis. The complex associates with centromeric DNA sequences that are usually species-specific. In plant species,
Kiyotaka eNagaki +4 more
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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
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Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis in Heliophila (Brassicaceae)
Frontiers in Plant Science, 2021 The unigeneric tribe Heliophileae encompassing more than 100 Heliophila species is morphologically the most diverse Brassicaceae lineage. The tribe is endemic to southern Africa, confined chiefly to the southwestern South Africa, home of two biodiversity
Mert Dogan +16 more
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Linear time algorithms for finding and representing all the tandem repeats in a string [PDF]
, 2004 Gusfield D, Stoye J. Linear time algorithms for finding and representing all the tandem repeats in a string. Journal of computer and system sciences. 2004;69(4):525-546.A tandem repeat (or square) is a string [alpha][alpha], where [alpha] is a non-empty ...
Stoye, Jens +2 more
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Identification of tandem repeat families from long-read sequences of Humulus lupulus.
PLoS ONE, 2020 Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe.
Katherine A Easterling +7 more
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Tandem repeats finder: a program to analyze DNA sequences [PDF]
Nucleic Acids Research, 1999 A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats
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Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris [PDF]
, 2010 Zakrzewski F, Wenke T, Holtgräwe D, Weisshaar B, Schmidt T. Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biology.
Zakrzewski, Falk +14 more
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