Biological sequences have long been known to contain many classes of repeats. The most studied repetitive structure is the tandem repeat where many approximate copies of a common segment (the motif ) appear consecutively.
In this talk, a more complex repetitive structure is presented. This repetitive structure is called a nested tandem repeat. It consists of many approximate copies of two motifs interspersed with one another.
Nested tandem repeats have been observed in the intergenic spacer of the ribosomal DNA gene in Colocasia esculenta. The question of whether such repeats can be found elsewhere in biological sequence databases is addressed and NTRFinder will be presented.
In order to compare two tandem repeat sequences an algorithm that aligns a hypothetical ancestral sequence of both sequences against each sequence is presented. This algorithm considers substitutions, deletions, and unidirectional duplication, namely, from ancestor to descendant. This algorithm has a quadratic time complexity.
Last modified: Tuesday, 16-Jul-2013 10:27:55 NZST
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