Repetitive sequences are abundant in the human genome. Different classes of repetitive DNA sequences, including simple repeats, tandem repeats, segmental duplications, interspersed repeats, and other elements, collectively span more than 50% of the genome. Because repeat sequences occur in the genome at different scales they can cause various types of sequence analysis errors, including in alig...

Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats can alter the function and/or expression of genes allowing organisms to swiftly adapt to novel environments. Importantly, some repeat expansions have a...

Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to study the distribution of tandem repeats in Nlrp1 gene, which is a critical gene to detect the invading pathogens in the immunologic mechanisms. The frequency o...

Motivation: Genomes are replete with short sequences repeated consecutively called tandem repeats. Reconstructing duplication histories for tandem repeats may yield valuable insights into their functions and the biological mechanisms of tandem repeat creation and extension. Results: We study the generalized neighbor-joining approaches for reconstructing tandem duplication history. We develop a ...

Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms (SNPs) have been the major focus of most large-scale comparative genomics studies to date. Here, we discuss a third, largely ignored, type of genetic variation, namely changes in tandem repeat number. Historically, tandem repeats have been designated as non functional "junk" DNA, mostly as a result of their highly unstable nature...

Glutamine tandem repeats are common in eukaryotic proteins. Although some studies have proposed that replication slippage plays an important role in shaping these repeats, the role of natural selection in glutamine tandem repeat evolution is somewhat unclear. In this study, we identified all of the glutamine tandem repeats containing four or more glutamines in human proteins and then estimated ...

Motivation: Genomes are replete with short sequences repeated consecutively called tandem repeats. Reconstructing duplication histories for tandem repeats may yield valuable insights into their functions and the biological mechanisms of tandem repeat creation and extension. Results: we design and implement a set of heuristic algorithms for reconstructing tandem duplication history with neighbor...

Tandem repeat patterns are very useful for biologists as they describes a pattern that helps to determine an individual's inherited traits. Tandem repeats can be very useful in determining parentage. These repeated nucleotides play a very important role to analyse and understand the various disorders available in cancer disease. Various data mining techniques like clustering, association analys...

Although there is no genetic diversity in isolates of Mycobacterium leprae, the variance of tandem repeats in the rpoT gene was recently demonstrated. We have typed clinical isolates of M. leprae in Korea using difference of the tandem repeats in the rpoT gene. Among 69 patients, 65 Korean isolates (94.2%) demonstrated four copies of the 6 bp tandem repeat (GACATC) in the rpoT gene, and inciden...