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This Week in Nucleic Acids Research : Jun 13, 2012

In Nucleic Acids Research Webserver Issue preprints published online in advance this week, more than two dozen groups present Web tools they've generated for genomics, proteomics, and more.

Researchers at Humboldt-Universität in Berlin present GeneView, a semantic search engine that is "built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts." The authors say this "semi-structured representation of biomedical texts enables a number of features extending classical search engines." For one, users can query entries using unique database identifiers, the Humboldt-Universität researchers say.

Investigators at Spain's Centro de Investigación Príncipe Felipe present a variant analysis tool dubbed Variant, which "reports information on the variants found that include consequence type and annotations taken from different databases and repositories," including the GWAS catalog, OMIM, and COSMIC. "Variant also produces a rich variety of annotations that include information on the regulatory — transcription factor or miRNA-binding sites, et cetera — or structural roles, or on the selective pressures on the sites affected by the variation," the authors write in Nucleic Acids Research.

And a team led by researchers at the University of Turku and Åbo Akademi University in Finland present what they call the BiForce Toolbox — a Web tool that aims "to address the demand for high-throughput analysis of pairwise epistasis in GWAS of quantitative and disease traits across all commonly used computer systems." Unlike other such tools, BiForce Toolbox "incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis," the authors write.