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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.  

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The Scan

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Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.