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Downloads and Upgrades: Apr 29, 2011

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This week, Biobase launched the BioKnowledge Transfer tool for functional annotation of next-generation sequences from uncharacterized genomes. The tool marks the firm’s second offering for the NGS market.

The tool, which is part of Biobase’s Proteome product, lets researchers input novel protein sequences and extract functional information based on those sequences.


SoftGenetics has released NextGene 2.14, the latest version of the company’s software for the analysis of sequence data from the Roche 454, Illumina, Ion Torrent Personal Genome Machine, and Applied BioSystems SOLiD System sequencing platforms.

The release includes enhanced transcriptome detection capabilities and a new pipeline tool for automation of NGS data analysis among other features.


Sage-N Research has released a new toolkit for developers of proteomics data analysis software to facilitate integration of its Sorcerer platform with independent software suites.

The toolkit comprises a web service application programming interface based on XML data formats that is accessible across a network, a cross-platform client library to access the API on Windows, Linux, and other operating systems, and a developer's toolkit including test beds, documentation, and other resources

The toolkit allows other applications, running on the Sorcerer platform or accessing it across the network from another computer, to specify and submit Sequest 3G searches, track and control submitted searches, and retrieve hits and scores. Sequest 3G is Sage-N Research's algorithm for MS-MS protein identification, with enhanced sensitivity for post translational modification analysis.


An iPhone application for EcoCyc is available for download from the iTunes store.

EcoCyc-Mobile provides streamlined mobile interaction for EcoCyc, a database that describes the genome and biochemical machinery of Escherichia coli K-12 MG1655.


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.