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Downloads & Upgrades: Dec 18, 2009


SoftGenetics has updated its NextGENe software for second-generation sequence analysis.

The new version is able to merge short paired-end reads from the Illumina Genome Analyzer and Life Technologies SOLiD platforms into contiguous reads of up to 300 or more base pairs with approximately 99 percent of the accuracy of Sanger sequencing, the company said.

The software also offers improved mapping via the DualRef system, which uses both normal and mutated references in the alignment process.

The company has also released a new browser for next-generation sequencing data that has been processed by NextGENe.

The viewer can be run on 32-bit desktop or laptop computers "for most data sets," the company said. It contains reference annotation and enables users to review, edit, and report analyses performed on the Roche 454 GS, Life Technologies SOLiD, and Illumina Genome Analyzer platforms.

CLC Bio has released the beta version of an improved version of its de novo assembler.

The assembler comes in two different editions: as a standalone command-line interface and as a graphical user interface through a plug-in for CLC Genomics Workbench.

The company said that the assembler is able to assemble a 37-fold coverage human genome with a 32 GB RAM computer in around seven hours.

The assembler supports data from "multiple" high-throughput sequencing instruments, including the Illumina Genome Analyzer, the Roche 454 platform, and Sanger sequencing.

The company said that it plans to release the final version of the assembler in the first quarter of 2010.

Oxford Gene Technology has launched CytoSure Interpret, a software package for analyzing oligonucleotide array comparative genomic hybridization data.

The software includes an "accelerate function" for automating data analysis workflows. Users can customize other functions, such as normalization, aberration detection, and report generation.

CytoSure Interpret integrates results with legacy data, confirmation probe information, and annotation tracks covering syndromes, genes, exons, copy number variants, and recombination hotspots. These tracks link to publicly available databases such as Decipher and the Database of Genomic Variants, OGT said.

Taverna 2.1 is available for download here.

New features include copy/paste, shortcuts, undo/redo, and drag-and-drop capabilities; an animated workflow diagram; secure web services support; R support, enhanced provenance, and integration with myExperiment.

Release 102 of the EMBL Nucleotide Sequence Database is now available from the European Bioinformatics Institute ftp server and other verified mirror sites.

Release 102, which contains data as of Nov. 26, includes 167,493,839 sequence entries comprising 266,361,987,641 nucleotides.

The Release 102 files total 125 GB compressed and 895 GB uncompressed.

Biopython 1.53 is available for download here.

Among other features, the release includes support for SQLite as part of the BioSQL interface and wrappers for the National Center for Biotechnology Information's Blast C++ tools.

The BioAnalytics Group has released BioPathwise DM version 2.4.

BioPathwise DM is a data-management tool that allows scientists with minimal computer skills to build knowledge repositories, the company said. Researchers can use the software to customize, capture data from multiple instruments in any format, work with third-party analytical tools, and collect analytical results in the same repository.

The system is also used to manage laboratory resources, such as tissue samples and consumables, together with experimental protocols, raw data, and analysis derived from the samples.

The company is developing BioPathwise DM in collaboration with the National Institute of Allergies and Infectious Diseases, the Program for Immune Modeling Experimentation (PRIME), and electronic laboratory notebook firm Contur Software.

Version 2.4 of the system is integrated with Contur ELN in order to automate the process of quickly capturing data and transmitting it into the PRIME repository.

The BioAnalytics Group said that it has also integrated a number of commonly used applications and laboratory devices with BioPathwise DM, including qPCR, image data, microarrays, and flow cytometry.

The Scan

Could Mix It Up

The US Food and Drug Administration is considering a plan that would allow for the mixing-and-matching of SARS-CoV-2 vaccines and boosters, the New York Times says.

Closest to the Dog

New Scientist reports that extinct Japanese wolf appears to be the closest known wild relative of dogs.

Offer to Come Back

The Knoxville News Sentinel reports that the University of Tennessee is offering Anming Hu, a professor who was acquitted of charges that he hid ties to China, his position back.

PNAS Papers on Myeloid Differentiation MicroRNAs, Urinary Exosomes, Maize Domestication

In PNAS this week: role of microRNAs in myeloid differentiation, exosomes in urine, and more.