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SRS 8.0, DNASIS GeneIndex, ENCODE portal, ORNL Genome Channel GrailExp, Progenesis 2D, Quantum 2.0

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Lion Bioscience has released SRS 8.0. The latest version of this integration platform offers web service capability; Java servlets; support for large sequence entries so that users can work with whole genomes in a single view; pre-defined queries and link views; and a quick search page that can be customized to show preferred queries.


MiraiBio said that it will launch version 3.5 of its DNASIS GeneIndex web-based data mining service on July 1. GeneIndex allows users to query more than 20 public and commercial biological databases using a single query search system. The system also retrieves sequence-related information from journal abstracts using weighted keywords and a proprietary search engine. Databases accessible through the system include Genbank/DDBJ/ EMBL, SAGEmap, UniGene, RefSeq, dbSNP, HomoloGene, TrEMBL, PubMed, KEGG, PDB, LocusLink, Swis-Prot, Prosite, and Pfam.


The University of California Santa Cruz genome bioinformatics group has released the ENCODE portal — a version of the UCSC Genome Browser tailored to the ENCODE (Encyclopedia of DNA Elements) project community. Resources include sequences for the current human assemblies (hg16, hg15, hg13, and hg12); sequences of the comparative species from ‘s Intramural Sequencing Center; tools for coordinate conversion between human assemblies; format de- scriptions for data submission; and contact information for help with submitting annotation data and analyses. Bulk downloads of the sequence and annotations are also available. The ENCODE portal is http://genome.ucsc.edu/encode.


Oak Ridge National Laboratory’s Life Sciences Division has released the ORNL Genome Channel GrailExp genes for NCBI human build 34.1 at http://compbio.ornl.gov/channel/index.html. The new version of the database was built with ORNL’s EXP6 gene-finding algorithm, which uses both ESTs and proteins for evidence of putative genes.


Nonlinear Dynamics has released a new version of its Progenesis 2D gel analysis software. The new release includes enhanced cross-stain analysis technology, which allows users to analyze multiplexed 2D gels. The software also includes INCA (Intelligent Noise Correction Algorithm), a proprietary algorithm developed to reduce image noise.


Quantum Pharmaceuticals has released Quantum 2.0, the latest version of its protein docking software. The company said it has improved the method of calculation of entropy loss for protein-ligand complexes and has also added a new model of the water environment along with electrostatic and Van der Waals energy contributions for flexible molecules.

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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.