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VIBE SDK, mpiBlast 1.2.0, CodeLink Informatics Solution, JDAS, Rfam 5.0, PhosphoSite, PopG, IMB Jena Image Library of Biological Macromolecules

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Incogen has released version 2.6 of the VIBE SDK (Visual Integrated Bioinformatics Environment Software Development Kit) for its VIBE data pipelining tool. The release includes new primer design tools, improved proxy and network configurations, and integration with the Sun Grid Engine, among other features. A free evaluation version is available at http://www.incogen.com/VIBE.


Los Alamos National Laboratory has released mpiBlast 1.2.0, a parallelized version of NCBI Blast, at http://mpiblast.lanl.gov. New features include alignments for translated searches, distributed sequence lookup, command-line options that match NCBI-Blast, and scripts to interface with the NCBI web front end via the PBS scheduling system.


Amersham Biosciences has upgraded its CodeLink Informatics Solution to include CodeLink Expression Analysis software — which acquires gene expression values from CodeLink Bioarray images —new workflows for the Scierra Microarray Laboratory Workflow System, and compatibility with the Scierra LWS DiscoveryHub integration platform.


A beta release of JDAS, an open source Java client library for the DAS (Distributed Annotation System) protocol, is available at http://www.xmlbio.org/jdas/index.html.


Rfam 5.0, a database of structure-annotated multiple sequence alignments, covariance models, and family annotation for 165 non-coding RNA families, is available at http://www.sanger.ac.uk/Software/Rfam/.


Cell Signaling Technology has launched PhosphoSite, a curated database of in vivo protein phosphorylation sites within human and mouse proteins. The database is freely available for education purposes, while proprietary information is available on a subscription basis.


Version 3.0 of PopG (formerly called Simul8) is available from the University of Washington at ftp://evolution.gs.washington.edu/pub/popgen/popg.html. The software simulates the evolution of a single locus in the presence of natural selection, mutation, migration, and genetic drift.


The IMB Jena Image Library of Biological Macromolecules at http://www.imb-jena.de/IMAGE.html has been updated to include data from the SCOP (Structural Classification of Proteins) database.

 

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The Scan

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Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.