BLAST Performance, SNP Analysis

The following examples are real-world application benchmarks recently performed by TimeLogic using several BLAST System configurations.

Ultra-Fast SNP Comparison with the Human genome

Algorithm: Tera-BLASTN

The aim of pharmacogenomics is to develop drugs that can be specifi cally targeted to a patient’s genotype group for high efficacy response and no side effects. Extensive progress in mapping SNPs, which are single nucleotide polymorphisms occurring in over 1% of a population, has brought rapid advances to this nascent field.

Identifying SNPs involved in novel disease targets, whether in a coding (cSNP) or regulatory (rSNP) capacity, is a key focus. With the help of population-based SNP studies, pharmacogenomic therapies and potential preventative approaches can be designed to address genetic risk factors. Comparing a large collection of SNP data to monthly Human genome updates can drain an institution’s computational resources. However, this is a critical task for research groups pursuing pharmacogenomics-based therapies.

To illustrate the BLAST System’s speed and efficiency for pharmacogenomics, population genetics and modern genetic toxicology, TimeLogic recently performed a private, large-scale benchmark. A BLASTN search was used to compare 1.7 million 25-mer nucleic sequences of proprietary SNP data (a total of 42,500,000 bases) against the human genome target of 3,099,043,584 bases.

Results: The DeCypher BLAST Solution completed the search in 28 hours, or 24X faster than a Linux cluster of 30 Pentium III 1 GHz CPUs. This test demonstrates performance equivalent to a server farm of over 700 CPUs.

Interested in further discussion of our benchmark data? Would you like to see custom benchmarks for your toughest bioinformatics bottlenecks? Contact a TimeLogic account executive today to learn more about DeCypher!