A new Plugin for automated spa typing analysis in BioNumerics
Sint-Martens-Latem, Belgium, August 18, 2006 – Applied Maths BVBA today announces the release of a new Plugin Tool for fully automated processing and epidemiological analysis of spa typing data in its premium software suite BioNumerics.
spa typing is a single-locus sequence technique used for epidemiological typing of Methicillin resistant Staphylococcus aureus (MRSA), based upon the the Staphylococcus protein A (spa). The so-called X-region of that gene is a polymorphic region containing short imperfect sequence repeats. These repeats are assigned unique codes and the combination of repeats in a staphylococcal strain results into a unique spa type.
Spa-typing has proven to be a very suitable technique for rapid, cost-effective and reproducible typing of MRSA in hospitals. Thanks to its portability, the technique is becoming widely used in international databasing and exchange networks.
The BioNumerics spa Typing Plugin features fully automated assembly from sequence trace files including history tracking and problem logging. The program assigns the repeat codes and identifies the spa types automatically. In case of ambiguous or unresolved assembly constructs, the program screens the database for the closest and most likely repeat and spa-type matches. BioNumerics provides powerful clustering and population modelling tools, which have been extended in version 4.6 to perform repeat comparison based upon the generalized DSI model. spa types can be compared by means of cluster analysis, Multi-Dimensional Scaling, phylogenetic inference and Minimum Spanning Tree modelling. The software also offers fast and powerful identification tools, allowing for new isolates to be screened against databases of extreme size.
Over 100 hospitals and public health institutions worldwide that perform epidemiological typing of Staphylococcus aureus are using BioNumerics. Many of these labs have already implemented spa typing for routine analysis or are planning to implement the technique. These labs will benefit from the ability of BioNumerics to acquire and compare all currently employed typing techniques and calibrate the results of spa typing against well established reference techniques such as PFGE.
The BioNumerics software provides a universal platform for databasing and analysis of 1D patterns, 2D gels, phenotype arrays, and DNA/protein sequences. The software provides powerful databasing, integrated networking and a wide range of data mining, clustering, identification, and statistical applications. BioNumerics is designed for lab-wide databasing and analysis of biodata in laboratories of any size and is in use in thousands of research sites worldwide. In addition, BioNumerics and its server application 'BioNumerics Server' are the cornerstones for numerous national and international research projects and epidemiological surveillance networks. PulseNet, a worldwide surveillance network for foodborne bacterial pathogens is by far the biggest achievement with BioNumerics, connecting many hundreds of public health labs in the United States, Canada, Europe, Latin America, the Far East, Australia and New Zealand.
About Applied Maths
Applied Maths develops cutting-edge software for the biosciences and offers a uniquely complete portfolio of Bioinformatics applications. The cornerstone for Applied Maths' success is BioNumerics, a software suite for integrated analysis of biodata that has grown into a universal platform for bio-databasing and analysis and is in use in thousands of research and diagnostics settings worldwide. The unique strength of Applied Maths lies in the non-obvious combination of bio(techno)logical and mathematical know-how. For more information, visit www.applied-maths.com.
Applied Maths and BioNumerics are registered trademarks of Applied Maths BVBA. Other company or product names mentioned are the trademarks of their respective owners.