BioNumerics version 6.1 released - Scaling up to chromosomes

Applied Maths NV today announces the release of version 6.1 of its flagship software suite BioNumerics. 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 public and private research sites worldwide. The software is referenced in more than 3,400 peer-reviewed scientific papers. 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 the foremost achievement with BioNumerics, connecting many hundreds of public health labs in the United States, Canada, Europe, Latin America, the Middle East, and Asia Pacific.

The highlight of BioNumerics version 6.1 is a new module for full chromosome comparison and alignment. The application uses a seed-based fast matching algorithm that allows continuous stretches of homology to be mapped between genomes, thus achieving a total genomic alignment that allows inversions, swaps, duplications, insertions and deletions to be aligned correctly. Matrices of nxn overall chromosome similarities can be calculated based upon pairwise alignments, thus enabling phylogenies to be calculated from full genomic homologies. The chromosome comparison module offers detailed side-by-side comparison and mapping of chromosomes, enabling the analysis of organization and functional behavior of genomes. Based on a selected template sequence, alignment of multiple chromosomes can be performed, which forms the basis for chromosome-based SNP analysis and dNdS analysis, all of which is available in the new module.

Besides this new application module, BioNumerics version 6.1 contains a large number of new interface and database enhancements and offers not less than 3 major new plugin applications:

The MIRU-VNTR plugin is based on the successful MLVA plugin and provides specific functionality for Mycobacterium interspersed repetitive units typing. The plugin synchronizes with the MIRU-VNTRplus server and allows types to be assigned automatically and new types to be assigned.

The SNP genotyping plugin performs automated and reliable SNP calling and genotyping of TaqMan® based SNP genotyping technology such as Applied Biosystems 7900HT, BMG Labtech 384-well microplate readers, and the Fluidigm Dynamic Array system.

The Diversilab plugin imports and analyzes patterns generated using the Diversilab™ system from bioMérieux ( BioNumerics stores the patterns as fingerprints in a database and provides smart on-the-fly normalization algorithms for automatically aligning the Diversilab patterns within a comparison.