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Genomics Workbench, dbSNP, SciTegic Enterprise Server 7.0, Bioconductor 2.2, NextBio, SimGlycan 2.51

CLC bio was previewing a beta version of the next-generation sequencing module for its Genomics Workbench software at the Bio-IT World Conference in Boston this week. The software performs alignment and assembly to a reference genome using reads from Applied BiosystemsSOLiD, Roche/454’s GS FLX, and Illumina’s Genome Analyzer.
Version 1.0 of the software is scheduled for release in late May, said Jan Lomholdt, vice president of CLC Bio. The full release will support data from the Helicos Heliscope and will also enable de novo assembly for short-read sequence data, he said.
The software runs on a laptop with 1 GB of RAM, though up to 4 GB may be required for large assemblies.
Future versions of the software will enable ChIP-Seq analysis and digital gene expression analysis with next-gen sequencing data, Lomholdt said.

The National Center for Biotechnology Information has released build 129 of dbSNP
In addition to the NCBI reference and Celera assemblies, dbSNP 129 is mapped to the new HuRef assembly, also called Human 36.3, which is the Venter diploid genome. 

Accelrys has released SciTegic Enterprise Server 7.0, the enterprise version of its Pipeline Pilot workflow software. Features of the new release include a service-oriented architecture environment, enterprise collaborative tools, interactive application building, and workflow parallelization.

Bioconductor 2.2 is available here. The release includes 35 new packages, bringing the total number of packages in the suite to 260. These packages are compatible with R 2.7.0.
A list of all package descriptions is available here.

NextBio has released a free version of its NextBio life science search engine here.
The search engine provides access to more than 10,000 experiments, 16 million articles, and “billions” of data points, the company said. Users can also import their own experimental data into the NextBio search engine in order to share it with the community.

Premier Biosoft has released SimGlycan 2.51, a new version of its MS/MS data analysis tool. The new release now analyzes glycopeptides in addition to released glycans, the company said.
SimGlycan matches the MS/MS spectra with its own annotated database to predict the structure of glycans and generate a list of all the probable glycans that are close to the experimental data.

Filed under

The Scan

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Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

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