TRedD--a database for tandem repeats over the edit distance.

Database : the Journal of Biological Databases and Curation
Dina Sokol, Firat Atagun

Abstract

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/

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Citations

Aug 28, 2012·Nucleic Acids Research·Elke SchaperMaria Anisimova
May 27, 2014·Database : the Journal of Biological Databases and Curation·Maria ChaleyNafisa Nazipova
Mar 14, 2013·Nordic Journal of Psychiatry·Lars HanssonBengt Svensson
Nov 17, 2006·BMC Genomics·Colm T O'Dushlaine, Denis C Shields
Jun 4, 2016·Journal of Laparoendoscopic & Advanced Surgical Techniques. Part a·Yoen T K van der LindenJelle P Ruurda
Apr 27, 2011·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Fan ZhangKing Ngi Ngan
Jan 20, 2018·Evidence-based Complementary and Alternative Medicine : ECAM·Hua Li, Hongying Liu
Jul 19, 2016·International Journal of Adolescent Medicine and Health·Fariba GhaderiMohammad Ali Mohseni Bandpei
Jul 27, 2011·Molekuliarnaia genetika, mikrobiologiia i virusologiia·Iu K KulakovE I Korenberg
Dec 20, 2012·Molekuliarnaia genetika, mikrobiologiia i virusologiia·Iu K KulakovM M Zheludkov
Oct 18, 2018·Nucleic Acids Research·Nicholas KinneyHarold R Garner

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Methods Mentioned

BETA
pull-down

Software Mentioned

mreps
TandemGraph
Internet Explorer
TRDB
UCSC
Firefox
JBrowse
TRedD
mySQL
ATRHunter

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