期刊
JOURNAL OF COMPUTATIONAL SCIENCE
卷 3, 期 5, 页码 328-334出版社
ELSEVIER
DOI: 10.1016/j.jocs.2011.10.001
关键词
Genomic sequence search; Sequence clusters; Lymphocytes and tissue sections; Labelling of vital cells
资金
- BMBF [FKZ 01|G07015G-Services@MediGRID, 13N11163 - COMBO-FISH]
- DFG
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. (C) 2011 Elsevier B.V. All rights reserved.
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