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eVOC 1.4, AnnHyb, GetDB, BioPerl 1.4, GenBank, GenomeKnowledgeBase, E-Cell, FABA 1.0, Nucleic Acids Research


The South African National Bioinformatics Institute, in collaboration with Electric Genetics, has released eVOC 1.4, a controlled vocabulary for describing the source of samples used in gene expression experiments. The ontologies, along with a total of 8,258 ontology-annotated human cDNA libraries, are available at

Version 4.9 of AnnHyb, software for working with and managing nucleotide sequences in multiple formats, is available at New features include compatibility with ClustalW multi-alignment and a new search utility for searching strings in sequence headers.

Genomining of Paris has upgraded its GetDB remote database download resource to provide access to the new UniProt database, which went live on Dec. 15, 2003.

BioPerl 1.4 is available at Three modules are available: bioperl-core (core BioPerl modules); bioperl-ext (C-compiled extensions); and bioperl-run (wrappers for external programs).

GenBank release 139.0 is now available from NCBI at ftp://ftp.ncbi. The release contains 36,553,368,485 base pairs and 30,968,418 entries, up by 953,747,014 base pairs and 1,149,021 sequence records from the October 138.0 release. Uncompressed, the 139.0 flat files require about 122 GB for the sequence files only. The ASN.1 version requires around 108 GB.

Version 7.0 of the GenomeKnowledgeBase is available at http://www. The latest version of the curated pathway resource includes 661 referenced human proteins organized into 62 pathways.

E-Cell version 3.1.100 is available at New features include a model editor, an SBML importer, and new dynamic modules.

Chang Bioscience has released FABA 1.0 (Functional Analysis by Association), a software package to visualize data from multiple gene expression data sets. The software is available with 64 pre-loaded human microarray data sets or 108 mouse data sets at a price of $195 for non-profit research groups or $225 for commercial groups. Further information is available at http://www.

Nucleic Acids Research has published its annual database issue, which includes papers describing 548 molecular biology data resources. The issue is freely available, even for non-subscribers, at http://nar.oupjournals. org/content/ vol32/suppl_1/.

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The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.