Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Rapid Large-Scale Oligonucleotide Selection for Microarrays
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
An efficient algorithm for finding gene-specific probes for DNA microarrays
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
A fast preprocessing algorithm to select gene-specific probes of DNA microarrays
FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics
Approximating border length for DNA microarray synthesis
TAMC'08 Proceedings of the 5th international conference on Theory and applications of models of computation
Hardness and approximation of the asynchronous border minimization problem
TAMC'12 Proceedings of the 9th Annual international conference on Theory and Applications of Models of Computation
Fast algorithms for selecting specific siRNA in complete mRNA data
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Space pruning monotonic search for the non-unique probe selection problem
International Journal of Bioinformatics Research and Applications
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The oligo microarray (DNA chip) technology in recentyears has a significant impact on genomic study. Manyfields such as gene discovery, drug discovery, toxicologicalresearch and disease diagnosis, will certainly benefitfrom its use. A microarray is an orderly arrangement ofthousands of DNA fragments where each DNA fragment isa probe (or a fingerprint) of a gene/cDNA. It is importantthat each probe must uniquely associate with a particulargene/cDNA. Otherwise, the performance of the microarraywill be affected. Existing algorithms usually select probesusing the criteria of homogeneity, sensitivity, and specificity.Moreover, they improve efficiency employing some heuristics.Such approaches reduce the accuracy. Instead, wemake use of some smart filtering techniques to avoid redundantcomputation while maintaining the accuracy. Basedon the new algorithm, optimal short (20 bases) or long (50or 70 bases) probes can be computed efficiently for largegenomes.