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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 +7 more sources
Human tandem repeat sequences in forensic DNA typing [PDF]
Legal Medicine, 2005 It has been 20 years since the first development of DNA fingerprinting and the start of forensic DNA typing. Ever since, human tandem repeat DNA sequences have been the main targets for forensic DNA analysis. These repeat sequences are classified into minisatellites (or VNTRs) and microsatellites (or STRs).
Tamaki, Keiji, Jeffreys, Alec J.
core +9 more sources
Statistical approaches to detecting and analyzing tandem repeats in genomic sequences [PDF]
Frontiers in Bioengineering and Biotechnology, 2015 Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions, and can be associated with virulence, resistance and infectious ...
Maria eAnisimova +3 more
doaj +5 more sources
Detection of Recombination in Variable Number Tandem Repeat Sequences [PDF]
S. Afr. Comput. J., 2007 Tandem repeats are repeated sequences whose copies are adjacent along the chromosomes. They account for large portion of eukaryotic genomes and are found in all types of living organisms. Among tandem repeats, those with repeat unit of middle size are called minisatellites. These loci depart from classical loci because of the propensity to vary in size
Adebiyi, Ezekiel, Rivals, Eric
core +5 more sources
TRviz: a Python library for decomposing and visualizing tandem repeat sequences. [PDF]
Bioinform Adv, 2023 Abstract 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 the motif composition of the TR sequences.
Park J +3 more
europepmc +5 more sources
Finding approximate tandem repeats in genomic sequences [PDF]
Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04, 2004 An efficient algorithm is presented for detecting approximate tandem repeats in genomic sequences. The algorithm is based on a flexible statistical model which allows a wide range of definitions of approximate tandem repeats. The ideas and methods underlying the algorithm are described and its effectiveness on genomic data is demonstrated.
Ydo Wexler +3 more
openaire +2 more sources
IMPACT OF TANDEM REPEATS ON THE SCALING OF NUCLEOTIDE SEQUENCES [PDF]
International Journal of Bifurcation and Chaos, 2006 Techniques such as detrended fluctuation analysis (DFA) and its extensions have been widely used to determine the nature of scaling in nucleotide sequences. In this brief communication we show that tandem repeats which are ubiquitous in nucleotide sequences can prevent reliable estimation of possible long-range correlations. Therefore, it is important
Radhakrishnan Nagarajan +1 more
openaire +2 more sources
Locating tandem repeats in weighted sequences in proteins [PDF]
BMC Bioinformatics, 2013 Abstract A weighted biological sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. We attempt to locate all the tandem repeats in a weighted sequence. A repeated substring is called a tandem repeat if each occurrence of the substring is directly adjacent to each other.
Zhang, Hui +2 more
openaire +5 more sources
STRING: finding tandem repeats in DNA sequences [PDF]
Bioinformatics, 2003 Abstract Motivation and results: The importance of Tandem Repeats in some genomes is now well established. We have reported elsewhere some interesting new results obtained by means of a preliminary program for finding Tandem Repeats in DNA sequences, together with a brief description of the basic ideas of the algorithm.
ALUFFI PENTINI, Filippo +2 more
openaire +3 more sources
Tandem repeat copy-number variation in protein-coding regions of human genes [PDF]
, 2005 BACKGROUND: Tandem repeat variation in protein-coding regions will alter protein length and may introduce frameshifts. Tandem repeat variants are associated with variation in pathogenicity in bacteria and with human disease.
O'Dushlaine, Colm T. +7 more
core +1 more source