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DNA tandem repeats (TRs) are ubiquitous genome features which consist of two or more adjacent copies of an underlying pattern sequence. The copies may be identical or approximate. TRs can be highly mutable with respect to the number of adjacent copies (copy number), with mutation rates orders of magnitude higher than those of SNPs. TRs are known to directly cause more than a dozen human neurological syndromes, are associated with other diseases, may have regulatory functions, and are useful genetic markers due to their high mutation rates.

Whole genome sequencing provides the raw material for identifying and studying, for the rst time on a genome-wide scale, those TRs which are inherently variable. In this paper we describe the VNTRseek pipeline for discovery of minisatellite TR variants, and its application to the 454 high-throughput sequencing data from the Watson and Khoisan genomes. A minisatellite TR, for the purposes of this study, has a pattern size 7 nucleotides. A VNTR, or Variable Number of Tandem Repeats, is a TR locus for which more than one allele has been observed, with each allele having a distinct copy number. Our pipeline maps reads to a set of reference TRs and then identies those references which appear to be VNTRs.


Send any questions or comments to: Yozen Hernandez.

Last updated: July 19, 2015