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Downloads and Upgrades: May 20, 2011


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

Pfizer-BioNTech Seek Full Vaccine Approval

According to the New York Times, Pfizer and BioNTech are seeking full US Food and Drug Administration approval for their SARS-CoV-2 vaccine.

Viral Integration Study Critiqued

Science writes that a paper reporting that SARS-CoV-2 can occasionally integrate into the host genome is drawing criticism.

Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.