Thursday, 15 November 2007
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Cartesian Gridspeed Releases Updated Version of SLIM Search For Advanced Genomic Research

Released as SLIM Search 1.3, Cartesian Gridspeeds latest offering promises great things, most significantly, searches performed up to 10,000 times faster than a fully optimized BLAST, the standard tool of the industry. To give a clear picture of this speed-bump, Cartesian claim  that a human genome  can be remapped in a few hours on a desktop workstation instead of months on a multimillion dollar computer cluster using BLAST. These are bold claims indeed, fortunately they are backed up by results presented in a white paper freely available on the SLIM Search website.

The latest version offers several new features, including platform support for Solaris 10 (32 bit and 64 bit) and installer support for RPM (Red Hat Package Manager), Linux and Sun Solaris 10. Corrected reported default settings and handling discrepancies for adjusting defaults to better match BLAST parameters are also included.

Features suited for Comparative Genomics, Genome Assemblies, Orthogonal Gene Mapping, Phylogenetics and  SNP Analysis including the ability to search all possible interactions and reciprocal pair-wise matches and whole genomes should also prove to be of use.

Additionally, SLIM Search employs the alignment mode of Blast to calculate trusted statistics, gap penalties, alignments and provide options to improve the methods.

Taking all these features into account along with the additional ability to deliver daily updates of an orthogonal-comparison, comparative-genomics database of every known gene on a single PC and sensitivities comparable with BLAST, the latest version of SLIM Search looks ready for much wider application in the genomics industry.

Cartesian also point out that additional gains are made through decreased hardware requirements and associated savings in maintenance costs and power usage. A factor of increasing importance in an evermore environmentally conscious society.  

Image
Screenshot taken from SLIM Search version1.3 displaying projects organized by subject (dataset searched against, same term as in BLAST) and query on the left and results from a Slim search (slimp- equivalent to blastp) with the mouse RSK1 protein kinase amino acid sequence on the right. Image courtesy of SLIM Search.


System Requirements:
SLIM Search can be run on any computer, but it is highly RAM dependent. The producers of the product test SLIM Search on Pentium laptops with 512 MB of RAM and suggest that most databases like Eukaryotic genomes, Unigenes, and Swissprot can be run with less than 4 GB of RAM.

To estimate the RAM requirements for the size of any given subject database SLIM Search offers the following formula as a guide: R=24D/k (where R=RAM, D=Database size in nucleotides or amino acids, and k=word size).

SLIM Search runs on 32 bit machines and single processors but has improved performance on 64 bit machines and with dual CPUs.

Additionally, SLIM Search 1.3 can run on any platform capable of running JAVA version 1.5

Pricing and Availability:
SLIM Search 1.3 is available immediately, directly from the SLIM Search website.
Prices start from US$199.00 for a single core academic license, with discounts available for multiple licenses. Trial software is also available for download from the SLIM Search website.

>> www.slimsearch.com

 
 

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