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Downloads and Upgrades: Sep 16, 2011


SoftGenetics has added a new capability to its NextGENe software that generates a list of possible causative mutation candidates when used with the tool's existing filtering capabilities. The new functionality can be used to find variants in rare disease studies and other types of experiments.

JMP Genomics has added new capabilities to its genomics and clinical software packages.

Among other updates, JMP Genomics 5.1 now includes a suite of tools for constructing and visualizing linkage maps, import routines for standard data formats, and new methods for analyzing and summarizing rare variants across loci or pathways.

JMP Clinical 3.1 now automatically creates patient narratives for each subject in a clinical trial that experiences a serious adverse event and saves them as a rich text format file. It also uses multiple testing methods, such as the double false discovery rate procedure, to reduce the risk of over-reporting adverse events.

The genome browser team at the University of California, Santa Cruz, has added several new features to the UCSC Genome Browser to help users configure and navigate its annotation tracks window.

Updates to the tool include automatic image resizing, improvements to the browser's drag-zoom navigation, and the ability to reorder groups of tracks, among other features.

This week, Integromics launched SeqSolve 2.0, the latest version of its analytical solution for next-generation sequencing data.

The release includes custom and proprietary annotations as well as new applications for ChIP-seq and RNA-seq analyses, including alternative splicing, new gene discovery, and transcript-level differential expression.

LabKey Software has released LabKey Server 11.2.

Updates to the software include new tools to create time visualizations as well as to track and find study data with custom subject groups. Users can also organize folders with a drag-and-drop graphical user interface, import dataset and specimen data, and integrate the server with existing systems.

RefSeq Release 49 is now available via FTP.

This release incorporates genomic, transcript, and protein data available as of Sept. 7, and includes 18,236,994 records, 13,137,813 proteins, 2,679,762 RNAs, and sequences from 16,248 different organisms.

Release 109 of the European Nucleotide Archive/EMBL-Bank is available from the European Bioinformatics Institute's ftp servers and several mirror sites.

Full release notes are available here.

DNAStar has released Lasergene 9.1

The release includes desktop computer support for genome-wide association studies using next-generation sequence information and it integrates protein sequence, structure, and bioinformatic method capabilities. The tool also helps users identify structural variants and provides information from both dbSNP and the Catalogue of Somatic Mutations in Cancer for many organisms.

Ensembl 64 is available here

This release includes assemblies for lamprey, Petromyzon marinus, and Tasmanian devil, Sarcophilus harrisi. It also includes updates to the cow and human assemblies and new regulation data for human and mouse among other updates.

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.