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GD Phylosopher, MGI 2.6., BioJava.

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GeneData has released version 3.5 of its GD Phylosopher system for the prediction of gene function based on the comparison of complete genomes.

GD Phylosopher 3.5 comes with the 47 microbial and higher eukaryotic genomes that are publicly available to date. The release also offers a proprietary functional annotation database that acts as a functional encyclopedia of these genomes.

The system is able to supplement this genomic information with data derived from in-house experiments, such as chemical data, high-throughput screening data, or proprietary phenotype data.

Other features include tools to understand biochemical reactions, pathways, and regulatory networks as well as an expression browser that enables the analysis of gene expression data from microarray technologies in its genomic context.

The Mouse Genome Informatics Group at the Jackson Laboratory has announced the release of MGI 2.6.

The new release of the mouse genome database, available at www.informatics.jax.org, includes links to Locus Link, RefSeq, and Interpro databases; a “your input welcome” button for sending marker or allele corrections to user support; new rules and guidelines for genes, alleles, and mutation nomenclature; and links from the MGI help documentation to the glossary.

The Mouse Genome Informatics Group is also releasing information on 21,076 mouse cDNA clones as part of its collaboration with the Genome Exploration Research Group of the Riken Institute of Physical and Chemical Research in Japan.

The Riken clone annotations are fully integrated into MGI and are accessible through standard query forms. The cDNAs represent a total of 15,294 genes, 12,905 of which are new genes to MGI.

The 1.1 release of BioJava is now available. New features include parsers for Blast and Fasta output and PDB files, feature interfaces for modeling gene structures, support code for making assemblies of biological sequences, and an experimental client for the Distributed Annotation System, a client-server system where a single client integrates information from multiple servers.

BioJava 1.1 can be downloaded from www.biojava.org/download/binaries.

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