TRedD--a database for tandem repeats over the edit distance.
A 'tandem repeat' in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition based upon the concept of 'evolutive tandem repeats'. In addition, we have developed a tool, called TandemGraph, to graphically depict the repeats occurring in a sequence. This tool can be coupled with any repeat finding software, and it should greatly facilitate analysis of results. Database URL: http://tandem.sci.brooklyn.cuny.edu/
Sokol
Dina
D
Department of Computer and Information Science, Brooklyn College of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA. sokol@sci.brooklyn.cuny.edu
Atagun
Firat
F
D000465:Algorithms; D001483:Base Sequence; D002880:Chromosomes, Human, Pair 11 / Q000235:genetics; D002888:Chromosomes, Human, Pair 19 / Q000235:genetics; D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D015894:Genome, Human; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000706:statistics & numerical data; D020080:Tandem Repeat Sequences