Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
429432 | Journal of Computational Science | 2012 | 7 Pages |
Abstract
For the selection of short triplex forming oligonucleotides for COMBO-FISH hybridisations used in research and medicine for 3D-structure investigations of the nucleus, the human genome has to be scanned for polypurine or poly-pyrimidine sequences which colocalise at the desired genomic region. Further binding sites of the selected oligonucleotides are required not to cluster anywhere else. We present an implementation of algorithms which design such oligonucleotide sets and exemplify the existence of COMBO-FISH probe sets by designing labelling sets for 29 genes and subsets thereof. The algorithms can be trivially parallelised and run on clusters, grids, and clouds.
Keywords
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Physical Sciences and Engineering
Computer Science
Computational Theory and Mathematics
Authors
Eberhard Schmitt, Jenny Wagner, Michael Hausmann,