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Downloads and Upgrades: May 20, 2011

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Version 53 of the Catalogue of Somatic Mutations in Cancer, COSMIC is now available.

The release includes several new genes bringing the number of fully curated cancer genes to 98 with a total of 81 curated fusion gene pairs.


This week, DNAstar released a version of its SeqMan NGen software that runs on the Linux operating system.

SeqMan NGen is a next‐generation software package for genome assemblies. The tool provides workflows for reference-guided assemblies, de novo and transcriptome assemblies, targeted re-sequencing and exome assemblies, and metagenome and population assemblies.

It also provides analysis tools for single nucleotide polymorphism and genotype calling, and can analyze coverage depth, group contigs into scaffolds, and annotate consensus sequences.


The Max Planck Institute for Informatics has released RINalyzer and RINerator, two new software tools that support automated generation, visualization, and interactive analysis of residue interaction networks.

RINalyzer combines the 3D structure view of a protein with its network representation. The software is complemented by the large online database called RINdata that contains over 50,000 precomputed RINs for most protein structures in the publicly available Protein Data Bank.

It provides methods to identify structurally and functionally important protein residues and to explore the impact of residue substitutions. The tool also computes a comprehensive set of weighted network centrality measures and supports the comparison of protein structures. It is available as a java plugin for Cytoscape.

The command-line tool, RINerator, can be used to generate RINs from protein structures in the PDB.


The Scan

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.