SNP / Oligo Matching

Comparing short sequences to a genome database is important for minimizing non-specific hybridization in microarray probe design. Tera-Probe™ offers significant advantages compared to other oligo search methods.

Tera-Probe combines the performance of Tera-BLAST with efficient Smith-Waterman alignment methods to identify oligonucleotide sequences across a genome. Tera-Probe surpasses NCBI BLAST sensitivity and matches Smith-Waterman results, yet offers much greater throughput.

Our DeCypher^® systems can run Tera-Probe faster than thousands of CPU cores running Smith-Waterman, making these solutions ideal for research teams mapping SNP databases, designing microarray probes, and designing RNA interference experiments.

Related Scientific Citations

Below is a short list of some recent DeCypher citations for SNP or Oligo Matching applications. For the complete list, please visit our citations page here.

1. Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa
   Jun Wang, Derek J Lydiate, Isobel AP Parkin, Cyril Falentin, Régine Delourme, Pierre WC Carion and Graham J King
   BMC Genomics 2011, 12:101.
2. Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation.
   John R. Garbe, Christine G. Elsik, Eric Antoniou, et al.
   Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 453638, 11 pages.
3. A Brassica Exon Array for Whole-Transcript Gene Expression Profiling
   Christopher G. Love, Neil S. Graham, Seosamh Ó Lochlainn, Helen C. Bowen4, Sean T. May, Philip J. White, Martin R. Broadley, John P. Hammond, Graham J. King
   PLoS ONE (2010), 5(9): e12812.
4. A robust linkage map of the porcine autosomes based on gene-associated SNPs
   Vingborg RKK, Gregersen VR, Zhan B, Panitz F, Hoj A, Sorensen KK, Madsen LB, Larsen K, Hornshoj H, Wang X, Bendixen C
   BMC Genomics 2009, 10:134 (27 March 2009)
5. A Snapshot of CNVs in the Pig Genome
   Fadista J, Nygaard M, Holm L-E, Thomsen B, Bendixen C
   PLoS ONE (2008) 3(12): e3916
6. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
   Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob H. Havgaard, Søren Brunak, Merete Fredholm, and Christian Bendixen
   Bioinformatics, Jul 2007; 23(13):i387-i391