Tera-Probe™ for sensitive, genomic mapping of short-read data and oligonucleotides

Tera-Probe™, part of the Tera-BLAST suite, combines the performance of Tera-BLAST¹ with efficient Query-Global Smith-Waterman alignment 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 at a much higher rate than software Smith-Waterman (SSEARCH), making these solutions ideal for research teams designing microarray probes, mapping SNP databases and designing RNA interference experiments.

Sensitive Remapping of Short-Read Sequence Data

Tera-Probe is an ideal tool for secondary mapping of next-gen sequence data. Existing algorithms are sufficient to map exact matches, and 1-2 mismatch 36-mers to the genome, but by remapping with Tera-Probe, you can increase the overall number of mapped reads due to higher tolerance for gaps, insertions and mismatches. This saves time, sample prep costs, and makes your sequencing process more efficient.

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 30 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 thousands of times faster than Smith-Waterman on one CPU core.
• 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
• Included with the Tera-BLAST module for DeCypher
• Also included with the CodeQuest workstation

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!