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Bioconductor 2.0, PhosphoMotif Finder, SXOligosearch, SynaSearch, Chemical Shift Query, Sentient Suite, Your Favorite Gene

Bioconductor 2.0 is available here. The release includes 36 new packages and many improvements and bug fixes to existing packages. The 214 packages in Bioconductor 2.0 are compatible with R 2.5.0, which was released on April 24. 

Johns Hopkins University’s Human Protein Reference Database project has released PhosphoMotif Finder, a database of known kinase/phosphatase substrates as well as binding motifs that are curated from the published literature.
HPRD now contains about 16,000 phosphorylation sites described in the literature, and PhosphoMotif Finder enables researchers to find potential phosphorylation sites in any protein of interest, according to the Hopkins developers.

Synamatix has launched two software products designed for analyzing data from next-generation sequencing instruments.
The first, SXOligosearch, is designed to map short sequences such as reads from the Illumina Genome Analyzer or oligonucleotide microarray probes.
The second is an updated version of the company’s SynaSearch sequence searching software that has been “modified to process and map reads from the GS20 and FLX platforms from 454,” the company said.

The Biological Magnetic Resonance Data Bank at the University of Wisconsin has released a Chemical Shift Query tool, which allows users to create tables of chemical shift information by specifying the residue of a protein or nucleic acid.

IO Informatics has released an updated version of its Sentient Suite, which includes three new modules: WebQuery, which enables users with no database expertise to query and browse multiple data sources from any location using a web browser; Process Manager, a drag-and-drop workflow platform for project management; and Knowledge Explorer, a data-modeling system based on semantic web technologies.

Sigma-Aldrich has released Your Favorite Gene, a web-based search tool that matches genes of interest against Sigma-Aldrich research products and public databases. The search engine is able to match 150,000 shRNAs, 725,000 siRNAs, 4,000 antibodies, proteins and kits, and 1,000 bioactive small molecules to specific genes of interest. The tool also provides integrated links to several public databases, such as the Human Protein Reference, NCBI Entrez Gene, and Cytoscape.  

Filed under

The Scan

More Boosters for US

Following US Food and Drug Administration authorization, the Centers for Disease Control and Prevention has endorsed booster doses of the Moderna and Johnson & Johnson SARS-CoV-2 vaccines, the Washington Post writes.

From a Pig

A genetically modified pig kidney was transplanted into a human without triggering an immune response, Reuters reports.

For Privacy's Sake

Wired reports that more US states are passing genetic privacy laws.

Science Paper on How Poaching Drove Evolution in African Elephants

In Science this week: poaching has led to the rapid evolution of tuskless African elephants.