BIOINFORMATICS

Nexus Copy Number Version 4

27 April 2009

BioDiscovery

BioDiscovery has released Nexus Copy Number Version 4, a platform-independent and efficient application for DNA copy number analysis of microarray-derived data. This latest version of the software offers many new features including a new algorithm for SNP arrays that combines log ratio and B-allele frequency values to segment the genome, detection of loss of hetrozygosity (LOH) and allelic imbalance calls for SNP array data, predictive power analysis for continuous data types, a query tool for listing genomic events for multiple genes or regions, and a one-click data loading tool.

Nexus Copy Number can integrate and process together, in a single project, data from commercial array platforms such as Agilent, Affymetrix, Illumina, Roche NimbleGen, as well as custom arrays. The software is applicable to many flavors of studies from focused projects of a cytogeneticist to large scale cancer studies. BioDiscovery is attuned to such different needs and offers Nexus Copy Number in two editions: Standard and Discovery.

The Standard Edition has all necessary tools for copy number analysis of CGH and SNP arrays including customisable reports listing aberrant regions and copy number and allele event calls, minimum regions of aberration among a set of samples, individual sample results, and includes a genomic browser with customisable annotation tracks for such items as genes, CNVs, exons, probes, and genetics diseases/disorders, and project-wise gene and region-based queries.

The Discovery Edition adds features that aid in exploration of data for more research-based use. These include clustering based on similar aberration profiles, identification of statistically different regions of change between sample sub-groups, gene ontology enrichment analysis, survival analysis and integration of external data such as gene expression.

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