Tera-Probe™ for sensitive, high-throughput oligonucleotide searches

Tera-Probe™ (pdf brochure) combines the performance of Tera-BLAST¹ with efficient Smith-Waterman alignment methods to identify oligonucleotide sequences across a genome. Tera-Probe exceeds NCBI BLAST² sensitivity and matches Smith-Waterman³ results, yet offers much greater throughput.

Both DeCypher® and CodeQuest™ biocomputing systems process Tera-Probe faster than sixteen thousand individual CPUs running Smith-Waterman, making these solutions ideal for research teams designing microarray probes, mapping SNP databases and designing RNA interference experiments

Selecting Optimal Microarray Probe Sequences

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

Smith-Waterman

• Often used to screen potential probe sequences, as it comprehensively explores all possible pairwise alignments to select an optimal local alignment.
• Smith-Waterman software (ssearch) is slow even on fast CPUs, with processing limited to 20 million cell comparisons per second per CPU.

NCBI BLAST

• Uses heuristic shortcuts to focus on anchor regions which share some core similarity, resulting in faster searches at the expense of sensitivity.
• May miss hits when multiple short gaps or mismatches occur between anchor regions

Tera-Probe

• Processes oligonucleotide search pipelines at 330 billion cell comparisons per second, or 16,500x faster than Smith-Waterman on 1 CPU.
• Requires only the space, power and cooling of a single workstation or server
• Can be scripted into your analysis pipelines
• Forces the entire oligo query to align to local target loci to ensure that all potential hybridization sites are examined
• Matches the sensitivity of Smith-Waterman software
• You can employ a custom scoring matrix to establish finely tuned scoring for matches and mismatch penalties
• Available with DeCypher Tera-BLAST and included with the CodeQuest workstation

Figure 1. Smith-Waterman (ssearch) was verified on a single CPU to compare 20 million cells per second. A single DeCypher Engine system compares 330 billion cells per second, for 16,500x the performance.

Figure 2. Comparing 10,000 oligonucleotide sequences (30-mers) to Unigene Mouse using DeCypher and GeneMatcher

A DeCypher system with 4 cards and 4 CPUs compares 10,000 oligos to Unigene mouse with Tera-BLAST in 1.5 hours. This requires 6 hours on a Paracel GeneMatcher2 system with 9 boards and 9 CPUs. Due to improved gap handling at the ends of each alignment, Tera-Probe identifies an additional 9,000 unique hits missed by GeneMatcher.

Applications such as microarray probe design, RNA interference, and mapping SNP sequences to a genome all require sensitive short sequence searches. Tera-Probe is ideally-suited to these challenges, with greater performance than any imlementation of Smith-Waterman. Tera-Probe is available as a module for the scalable DeCypher enterprise system and is also included on the CodeQuest biocomputing workstation.

For faster, more accurate results than CPU and cluster-based solutions, contact TimeLogic learn how Tera-Probe can improve your short sequence comparison pipelines. Tell us how you utilize oligo searches in your research and enter our drawing for an iPod® nano!

References

1. Luethy et al. Hardware and software systems for accelerating common bioinformatics sequence analysis algorithms. Biosilico 2(1), 2004
2. Altschul, SF, et al. Basic local alignment search tool. J Mol Biol 215(3), 1990.
3. Pearson, WR. Effective protein sequence comparison. Methods Enzymol. 266, 1996.

Contact a TimeLogic bioinformaticist today to learn more about Tera-Probe today!

Download Complete Tera-Probe brochure