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Downloads & Upgrades: Dec 5, 2008

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Researchers from Argonne National Laboratory, the University of Chicago, and San Diego State University have released MG-RAST, an open source system for automated processing of metagenomic sequence data.
 
MG-RAST, short for Meta Genome Rapid Annotation using Subsystem Assembly, generates phylogenetic and functional summaries of genomes by comparing the sequence against protein and nucleotide databases. It is based on the SEED framework for comparative genomics and designed for data from the Roche/454 platform.
 
Researchers can upload data sets in the file format generated by the instrument, either as raw reads or assembled contigs. The uploaded data are compared against a variety of known sequence databases, including rRNA and mitochondrial databases, and are screened for protein-coding genes.
 
The tool provides the data types needed for phylogenetic comparisons, functional annotations, binning of sequences, phylogenomic profiling, and metabolic reconstructions.
 

 
Symyx Technologies announced that its chemical drawing application Symyx Draw 3.1, is available for download at no charge for academic and non-commercial personal use here.  
 
Symyx Draw 3.1 helps scientists draw and edit chemical structures and reactions and facilitates collaborative searching, viewing, registering, and archiving of scientific information, the company said.
 

 
LabKey Software, a provider of open-source software for large-scale, collaborative research projects, has released LabKey Server v8.3.
 
According to LabKey, the updates make the tool more customizable for lab researchers, administrators, and developers involved in infectious disease and cancer research and facilitate integrating, sharing, and analyzing complex biological data
 
Some aspects of the software include: high-throughput, customizable batch processing; improved quality control of study data; flexible options for using and displaying data in LabKey Server; improved integration with existing flow cytometry tools; and improved site administration.
 

 
Rosetta Biosoftware announced the release of Elucidator system version 3.2, with major enhancements for support of SILAC and (14)N/(15)N labeling and phosphoproteomics, the company said.
 
The system's data management capabilities allow users to organize and analyze complex LC/MS expression data and new data analysis workflows will enable scientists to discover post-translational modifications of all types, including those related to phosphoproteomics, the company said. Metabolic labeling enhancements include support for SILAC and (14)N/(15)N labeling, expanding the differential expression toolkit.
 
The application supports “many” instrument vendors' raw files and universal database search engines, while providing support for multiple workflows, Rosetta said. It also provides a suite of advanced statistical analysis and visualization tools for data mining and discovery of proteins that are differentially expressed among different phenotypes or drug treatments.
 

 
GE Healthcare has introduced DeCyder 2D 7.0, a software package for analysis of 2D Fluorescence Difference Gel Electrophoresis, or 2D DIGE, experiments for detecting and quantitating biological differences in protein abundance between different samples. DeCyder 2D 7.0 applies a gel comparison method that introduces zero statistical error, the company said.
 
The software introduces fewer false positives/negatives due to a “unique co-detection algorithm,” GE said. It also enables linking of data from two or more datasets, increasing sample population to allow better differentiation between real and experimental variation.
 

 
The Sept. 2007 EquCab2 release of the horse genome is now available in the University of California, Santa Cruz, Genome Browser. The assembly was produced by the Broad Institute.
 
The horse draft genome has been sequenced to 6.8X coverage. Approximately 84 percent of the sequence has been anchored to chromosomes, which include autosomes 1-31 and sex chromosome X, UCSC said. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn," separated by gaps of 1,000 bp. The mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM."
 
More details about the current assembly are available on the Broad Institute’s Horse Genome Project website here.
 
Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server and downloads page.   

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