The detection of tandem repeats is important in biology and medicine as it can be used for phylogenic studies and disease diagnosis. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length. This paper presents results obtained by combining grey level spectrograms with a novel n...

We have developed a graphical tool to model regularities in biological sequences. TandemGraph enables a user to study and analyze string regularities. An important application of this tool is when used to model tandem repeats found within chromosomes. We have used TandemGraph to graphically represent the tandem repeats in the human genome found by a tandem repeats program called TRed. The tool ...

Local repetitions in genomes are called tandem repeats. A tandem repeat contains multiple, but slightly different copies of a repeated unit. It changes over time as the copies are altered by mutations, when additional copies are created by amplification of an existing copy, or when a copy is removed by contraction. Theses changes let tandem repeats evolve dynamically. From this statement follow...

We study the problem of detecting all occurrences of (primitive) tandem repeats and tandem arrays in a string. We first give a simple timeand space-optimal algorithm to find all tandem repeats, and then modify it to become a time and space-optimal algorithm for finding only the primitive tandem repeats. Both of these algorithms are then extended to handle tandem arrays. The contribution of this...

Tandem repeats are ubiquitous in the genome of organisms and their mutated forms play a vital role in pathogenesis. In this study, tandem repeats in Gastric Intrinsic Factor (GIF) of gastric parietal cells have been investigated using an in silico approach. Six types of the nucleotide tandem repeat motifs have been investigated, including mono-, di-, tri-, tetra-, pentaand hexanucleotide. The d...

Tandem repetitive DNA is highly abundant in eukaryotic genomes and contributes to transcription control and genome stability. However, how the individual sequences within tandem repeats behave remains largely unknown. Here we develop a collection of fission yeast strains with a reporter gene inserted at different units in a tandem repeat array. We show that, contrary to what is usually assumed,...

The evolutionarily conserved multisubunit THO complex, which is recruited to actively transcribed genes, is required for the efficient expression of FLO11 and other yeast genes that have long internal tandem repeats. FLO11 transcription elongation in Tho- mutants is hindered in the region of the tandem repeats, resulting in a loss of function. Moreover, the repeats become genetically unstable i...