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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 has(More)
We have performed the first genome-wide analysis of the Inverted Repeat (IR) structure in the human genome, using a novel and efficient software package called Inverted Repeats Finder (IRF). After masking of known repetitive elements, IRF detected 22,624 human IRs characterized by arm size from 25 bp to >100 kb with at least 75% identity, and spacer length(More)
The current explosion of stored information necessitates a new model of pattern matching, that of compressed matching. In this model one tries to nd all occurrences of a pattern in a compressed text in time proportional to the compressed text size, i.e., without decompressing the text. The most eeective general purpose compression algorithms are adaptive,(More)
Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA. It(More)
Some pathogenic bacteria are genetically very homogeneous, making strain discrimination difficult. In the last few years, tandem repeats have been increasingly recognized as markers of choice for genotyping a number of pathogens. The rapid evolution of these structures appears to contribute to the phenotypic flexibility of pathogens. The availability of(More)
Digitized images are known to be extremely space consuming. However, regularities in the images can often be exploited to reduce the necessary storage area. Thus, many systems store images in a compressed form. The authors propose that compression be used as a time saving tool, in addition to its traditional role of space saving. They introduce a new(More)
We seek to define sequence-based predictive criteria to identify polymorphic and hypermutable minisatellites in the human genome. Polymorphism of a representative pool of minisatellites, selected from human chromosomes 21 and 22, was experimentally measured by PCR typing in a population of unrelated individuals. Two predictive approaches were tested. One(More)
Recent proliferation of digitized data and the unprecedented growth in the volume of stored and transmitted data motivated the definition of the compressed matching paradigm. This is the problem of efficiently finding a pattern P in a compressed text T without the need to decompress. We present the first optimal two-dimensional compressed matching(More)