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Downloads & Upgrades: Apr 10, 2009


BioDiscovery has launched Nexus Copy Number Version 4, a platform-independent application for DNA copy-number analysis of microarray-derived data.

The new version includes a new algorithm for SNP arrays that combines log ratio and B-allele frequency values to segment the genome; detection of loss-of-heterozygosity 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 data from commercial array platforms from such firms as Agilent, Affymetrix, Illumina, and Roche NimbleGen, as well as custom arrays, BioDiscovery said.

The software is available in two editions: The standard edition enables copy-number analysis of CGH and SNP arrays including customizable reports listing aberrant regions and copy-number and allele-event calls, minimum regions of aberration among a set of samples, individual sample results, and a genomic browser with customizable annotation tracks. The discovery edition enables 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.

The European Bioinformatics Institute has released version 98 of the IntAct database. The current version comprises 189,489 binary interactions from 3,893 manually curated publications, including 57,290 proteins, 10,264 experiments, and 1,484 controlled vocabulary terms.

Biomatters has released version 4.6 of its Geneious software for managing, visualizing, and interpreting sequence data. New features include enhanced importing of all supported data types from a Vector NTI database; support for Gateway cloning functionality; improved import and export functionality for Sanger GFF annotations; and enhanced plasmid map visualization.

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