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Genome (in)stability at tandem repeats
Seminars in Cell and Developmental Biology, 2021Repeat sequences account for over half of the human genome and represent a significant source of variation that underlies physiological and pathological states. Yet, their study has been hindered due to limitations in short-reads sequencing technology and difficulties in assembly.
Elisa Balzano +2 more
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Folding and Misfolding of a PDZ Tandem Repeat
Journal of Molecular Biology, 2021Although the vast majority of the human proteome is represented by multi-domain proteins, the study of multi-domain folding and misfolding is a relatively poorly explored field. The protein Whirlin is a multi-domain scaffolding protein expressed in the inner ear. It is characterized by the presence of tandem repeats of PDZ domains.
Visconti, Lorenzo +5 more
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Tandem repeats finder: a program to analyze DNA sequences
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 ...
Gary Benson, Benson Gary
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An algorithm for approximate tandem repeats
2005A perfect tandem repeat within a string S is a substring r = r1,... r2l of S, for which r1 ... rl = rl+1 ... r2l. An approximate tandem repeat is a substring r = r1,..., rl′,... rl, for which r1,..., rl′ and rl′+1, ... rl are similar. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k ...
Gad M. Landau, Jeanette P. Schmidt
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Short Tandem Repeats and Genetic Variation
2010Single nucleotide polymorphisms (SNPs) are widely distributed in the human genome and although most SNPs are the result of independent point-mutations, there are exceptions. When studying distances between SNPs, a periodic pattern in the distance between pairs of identical SNPs has been found to be heavily correlated with periodicity in short tandem ...
Madsen, Bo Eskerod +2 more
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Clustering Tandem Repeats via Trinucleotides
2012 IEEE 12th International Conference on Data Mining Workshops, 2012Tandem repeats in DNA sequences are extremely relevant in biological phenomena and diagnostic tools. Computational programs that discover these tandem repeats generate a huge volume of data, which is often difficult to decipher without further organization.
Yupu Liang, Dina Sokol, Sarah Zelikovitz
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Classification of Tandem Repeats in the Human Genome
International Journal of Knowledge Discovery in Bioinformatics, 2012Tandem repeats in DNA sequences are extremely relevant in biological phenomena and diagnostic tools. Computational programs that discover these tandem repeats generate a huge volume of data, which is often difficult to decipher without further organization.
Yupu Liang +3 more
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The short tandem repeat locus D3S1359
Forensic Science International, 1998Short tandem repeats (STRs) are used by many laboratories throughout the world performing paternity testing or criminal casework. Nevertheless, many of the established STRs have obvious disadvantages such as low number of common alleles (e.g., hTPO, THO1) or alleles with frequencies of nearly 50% (e.g., hTPO, FES).
R, Pöltl, C, Luckenbach, H, Ritter
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A genomic view of short tandem repeats
Current Opinion in Genetics & Development, 2017Short tandem repeats (STRs) are some of the fastest mutating loci in the genome. Tools for accurately profiling STRs from high-throughput sequencing data have enabled genome-wide interrogation of more than a million STRs across hundreds of individuals.
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Reconstructing the duplication history of a tandem repeat.
Proceedings. International Conference on Intelligent Systems for Molecular Biology, 2000One of the less well understood mutational transformations that act upon DNA is tandem duplication. In this process, a stretch of DNA is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. Over time, the copies undergo additional mutations so that typically, multiple approximate tandem copies are present.
Gary Benson, Lan Dong
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