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eArray 3.5, Armadillo, Ensembl, caCORE, Pro Anvil Viewer, Kinase Knowledgebase, wEMBOSS

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Agilent Technologies has released eArray 3.5, which enables researchers to share their microarray design information with collaborators, at http://earray.chem.agilent.com/earray/login.do. The new version of the online application also provides access to Agilent's catalog array comparative genomic hybridization probes, and has also been expanded to allow researchers to upload their own aCGH probes. Agilent said that more than 300 users from 160 organizations worldwide have registered through eArray to date.


The Blueprint Initiative has released Armadillo, a new software tool for mapping linker regions and domain boundaries in proteins. Armadillo predicts domain and linker boundaries using a domain-linker propensity index that was constructed by comparing the amino acid composition of linkers in a non-redundant domain dataset. The index converts the amino acid sequence of a test protein into a numerical profile, providing scientists with a graphical view of domain boundaries, Blueprint said. The system is described in the current issue of the Journal of Molecular Biology [Dumontier et al. J. Mol. Biol. 2005, 350, 1061-1073], and is available at http://armadillo.blueprint.org.


Version 32 of Ensembl is available at http://www.ensembl.org. The new release includes the cow genome and updated zebrafish, mouse, and fly assemblies. The website has also undergone a major redesign in order to improve navigation and to make the code easier to extend and customize, according to the Ensembl development team.


The National Cancer Institute Center for Bioinformatics has released caCORE 3.0.1 and caCORE SDK 1.0.3 at http://ncicb.nci.nih.gov/core, a maintenance release for the NCI bioinformatics architecture. New features in the SDK include support for creating web services, for adding security, and for creating a write API.


Helyxzion has released version 3.0 of its Pro Anvil Viewer software for visualizing and analyzing DNA sequence data. According to the company, the web-based software can "depict protein structures of genes, reveal dominant and recessive genetic characteristics, compare multiple code strings quickly, and describe DNA, RNA and amino acid relationships."


Eidogen-Sertanty said it has upgraded its Kinase Knowledgebase (KKB) to include more than 390,000 unique kinase molecules and more than 160,000 structure-activity-relationship data points mined from approximately 1,900 journal articles and patents. The company said that the KKB is released quarterly and has a growth rate of more than 50,000 SAR data points and 90,000 unique structures per year.


Version 1.5 of wEMBOSS and version 1.3 of wrappers4EMBOSS are available at http://www.wemboss.org. New features in wEMBOSS 1.5 include a session indicator to identify which user is running wEMBOSS, and the ability to add notes to project results. The new version of wrappers4EMBOSS includes a codehop wrapper for selecting degenerated primers, and a muscle wrapper for multiple alignments.


Advanced Chemistry Development has launched ACD/Structure Design Suite, a software application that analyzes the physicochemical properties of a chemical entity or parent compound, and suggests subsequent biologically acceptable substitutions and structural modifications, leading to enhanced molecular physical properties, ADME characteristics, or environmental endpoints, the company said.

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