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Downloads and Upgrades: Mar 25, 2011


The Virginia Bioinformatics Institute has released GenoTHREAT — a software package that lets users detect the use of synthetic DNA as bioterrorism agents — under the Apache License Version 2.0.

GenoTHREAT implements the “best match” screening protocol method recommended by the federal government to minimize the risk that unauthorized individuals or those with malicious intent will obtain toxins and other potentially dangerous materials from DNA synthesis providers.

The software was developed by a team of students from Virginia Tech and ENSIMAG, an engineering school in Grenoble, France (BI 07/23/2010).

This week, MacVector released MacVector 12, software for DNA and protein sequence analysis.

Updates include click cloning enhancements that help users select restriction sites for clone construction, and improved navigation features for the graphical map feature, including multiple selection modes and the ability to zoom in and out of both circular and linear sequences using either the mouse or keyboard.

Other improvements include the ability to use mixed case residues in the editor and colors to emphasize regions or features of interest, design PCR primers, and select features for analysis across the circular origin, among other features.

Version 2.1 of the GeneMANIA plugin for Cytoscape has been released.

The updated plugin features reworked network descriptions to provide more provenance and linkouts, new elements for the network section in the XML report, as well as several bug fixes among other improvements.

The Protein Data Bank in Europe has launched a new, chemistry-based module for its PDB archive browser called PDBeXplore.

The compound-based browser lets users search for chemical compounds of interest by name and analyze all the PDB entries that contain that compound. Users can view information about protein fold families, possible quaternary structure(s) of the selected PDB entries, and Pfam families that are present in the
selected PDB entries among other types of data.

The National Center for Biotechnology Information has launched dbSNP build 133 for the cow genome as well as updates to the grape, macaque, and soybean genomes.

The complete data for build 133 can be found here in multiple formats.

The complete build summary for 133 is available here.

A total of 9,493,419 reference SNPs are in this release including more than 5 million new SNPs added since the last release.

Minor updates with no additional new annotations were performed on grape, macaque, and soybean to include these organisms in Entrez search and the FTP dumps.

This week, Accelrys launched Symyx Notebook v. 6.6, a multidisciplinary electronic lab notebook supporting scientists working in the chemistry, manufacturing, and controls area of drug development.

The notebook supports analytical, process, and formulation teams working in small- and large-molecule development, and enables cross-disciplinary teams to work collaboratively to move therapeutic substances and related information from research through development to early manufacturing using validated and compliant processes.

SRI International has released BioCyc Version 15.0 with updates to the EcoCyc and MetaCyc databases.

Updates to the EcoCyc database include a new metabolic pathway; an updated set of full-text Escherichia coli scientific articles; and new consensus sequences for 45 local transcription factors with three or less binding sites in the database, among other features.

The updated MetaCyc database now contains 37 new pathways for both plants and animals including sulfur metabolism, thyronamine signaling molecules, and plant biosynthetic pathways.

SRI also updated its Pathway Tools software to incorporate improvements to pathway layout algorithms, interactive tools for finding dead-end metabolites and choke-point analysis of metabolic networks, as well as new commands to find pathways and proteins by curation status, among other changes.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.