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Abstract:
We present a method for the automatic generation of oligonucleotide probe sets for DNA microarrays. This ap- proach is well suited particularly for specificity evaluation of designed probes in large data sets. Algorithms for probe preselection, hybridization prediction and probe selection are presented. Combinatorial techniques are introduced for the selection of probe sets of high differentiation ca- pability even from sequence databases of homologous con- served genes. These techniques include the automatic gen- eration of group specific probes and the design of exluding probes. A basic prototype was implemented including a shared memory parallelization and distribution. The principal applicability of our method to a database of very conserved sequence data was shown and the run-time performance estimated.
Reference:
Accurate method for fast design of diagnostic oligonucleotide probe sets for DNA microarrays A. Krause, M. Kräutner, H. MeierIn Proc. 17th International Parallel & Distributed Processing Symposium (IPDPS2003), Workshop on High Performance Computational Biology, 2003
Bibtex Entry:
@inproceedings{krause03accurate,
	Author = {Andreas Krause and Markus Kr{\"a}utner and Harald Meier},
	Booktitle = {Proc. 17th International Parallel & Distributed Processing Symposium (IPDPS2003), Workshop on High Performance Computational Biology},
	Title = {Accurate method for fast design of diagnostic oligonucleotide probe sets for DNA microarrays},
	Year = {2003}}