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Downloads and Upgrades: Nov 12, 2010


Ensembl 60 is available here.

The latest release includes data from the giant panda, new assemblies and genebuilds for zebrafish and rabbit, a new display for Gene Ontology terms, and improved navigation on Region in Detail, including autocompletion of gene display names.

DNA2.0 has launched a suite of free life science teaching tools for educators and students.

Included in the suite are the company's Gene Designer software and its Bioinformatics Toolbox.

This week, the National Center for Biotechnology Information launched dbSNP build 132.

The complete data for build 132 can be found here in multiple formats

The complete build summary for 132 is here

RefSeq 44 is now available via FTP from the National Center for Biotechnology Information.

This release incorporates genomic, transcript, and protein data available as of Nov. 7 and includes 16,421,261 records, 11,652,892 proteins, and sequences from 11,354 different organisms.

This week, BioDiscovery released Nexus Copy Number 5.1, the latest version of its DNA copy number analysis and visualization software.

According to the developers version 5.1 has an improved user interface, which lets the user review samples, identify possible pathogenic regions, compare the results with preprocessed samples, obtain annotations from external databases, and generate customized reports.

Also included in the release is the FASST2 segmentation algorithm, PennCNV processing, and support for Affymetrix OncoScan arrays.

This week, Life Technologies released BioScope version 1.3, the latest installment of its data analysis software.

BioScope provides users with workflow applications including MaxMapper mapping and pairing, BFAST integration, SAET Accuracy Enhancement, and several resequencing pipelines. The tool also lets users perform whole-transcriptome analysis, gene fusions and splice junction detection, and targeted resequencing among other capabilities.

Premier Biosoft International has launched lipid identification software called SimLipid that's aimed at supporting lipid mass spectrometric data interpretation.

According to the developers, SimLipid profiles lipids by matching the experimental MS spectra with those stored in its own database, which consists of 9 lipid classes and 1,948 lipid species. Next, the tool retrieves lipids from the database that correspond to the observed spectra and user's specified filter criteria.

In addition to the lipid's structure, the software also provides the lipid's ID, abbreviation, systematic name, category, mass, and chemical formula, as well as links to other databases including the Human Metabolome Database and the PubChem Substance database. In addition, users can query the database using the lipid's abbreviation, mass, chemical composition, or ID.

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.