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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


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

Los Alamos National Laboratory has released mpiBlast 1.2.0, a parallelized version of NCBI Blast, at 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

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

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 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 has been updated to include data from the SCOP (Structural Classification of Proteins) database.


Filed under

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.