Accelerate R&D Cycles with Prospector™
Grid-Powered Sequence Analysis
Prospector, a grid computing software package built specifically to address the widening "data and computation gap" in the bioinformatics field, lets users run analyses faster, easier, and more comprehensively than ever before. Prospector, built with patented software technology1 by Parabon Computation, is a suite of software tools that focuses the raw computing power of the Frontier Grid Platform to perform large dataset comparisons, such as genome-to-genome, genome-to-database, and database-to-database.
Until now, the main challenge for researchers running BLAST (Basic Local Alignment Search Tool) has been memory capacity and throughput. Specifically, BLAST processes information so quickly that it exhausts data stored in RAM. When more data is required for analysis, jobs get "stuck" when information is retrieved from hard disks, resulting in a slow and cumbersome computing process.
To avoid accessing hard disk drives, the answer to this problem has been to put entire databases into main memory. But as GenBank exceeds 85 billion nucleotides, this is an increasingly painful and costly solution — especially when hundreds of machines are involved. At the same time, it's essential to repeatedly search against the most current version of GenBank and other databases early in R&D to find the most promising targets.
The Solution: Break the Data Bottleneck
Prospector employs a novel approach to database division and analysis that actually turns the amount of data into an advantage on Frontier. How? By sending sets of query and database sequences of approximately equal total length to each machine, the search space is divided into searchable "squares".
This division minimizes the amount of data that needs to be sent to each computer in order for it to do a useful amount of work. Now, the total amount of main memory needed — which used to be linearly proportional to the number of machines — is now proportional to the square root of the number of machines. Prospector turns the quadratic nature of the problem to your advantage, both in disassembly and reconstruction.
Results You Can Count On
Prospector ensures the integrity of results by overlapping Eigen values. Get the results you expect and verify easily:
Proven Industry Algorithms
You can use Prospector to compare two libraries in FASTA or GenBank format using the Smith-Waterman or BLAST algorithm. Prospector performs the most valuable bioinformatic comparisons in a new way:
DNA-to-Protein (translated in all 6 frames)
Protein-to-DNA (translated in all 6 frames)
DNA-to-DNA (translated ina ll 36 frames)
NCBI BLASTblastp: Protein-to-Protein
blastx: translated DNA-to-Protein
tblastn: Protein-to-translated DNA
tblastx: translated DNA-to-translated DNA
Monitor Jobs Anytime, Quickly and Easily
Prospector's job controller provides a simple interface that allows you to quickly check the status of your job.
The Score Histogram provides a snapshot of your job's results.
Updated as the results from each task are received, the histogram illustrates the distribution of comparison scores.
1Blair, et al. Apparatus and method for providing sequence database comparison, US Patent 7,231,390, June 2007.