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Downloads and Upgrades: Dec 17, 2010


This week, DNAnexus launched the DNAnexus Exome Analysis application.

The application, which is accessible via the company’s cloud-based platform, lets users analyze exome sequence data in the cloud and determine whether regions of interest have been sequenced with sufficient coverage to allow for further analyses

The tool provides support for standard exome kits from Agilent and Roche NimbleGen as well as custom user-uploaded targets provided in BED file format and the company plans to support Illumina's TruSeq exome enrichment kits soon. In addition to user-uploaded datasets, DNAnexus also supports 20 reference genomes including bacteriophage Phi X 174 and rice (Oryza Sativa).

Elsevier and WebLib have launched HealthMash, an application that aims to provide researchers with biomedical concepts that are related to their searches including information on disorders, tests and diagnoses, treatments and drugs.

Powered by WebLib's Health Knowledge Base, the application uses a variety of semantic technologies and natural language processing tools and contains content from the National Library of Medicine's Medical Subject Headings Thesaurus, the Unified Medical Language System, and elsewhere.

The application is available on the SciVerse Applications beta website.

Cresset has released version 3.0 of FieldAlign, its cloud-enabled molecular design and 3D structure activity relationship software, which generates molecular comparisons that can be used to find the root causes of biological activity or inactivity.
Version 3.0 includes a command-line interface that supports scripting and workflow systems; incorporates a molecule table that enables filtering and sorting of lead molecules using imported data or standard physical properties, such as wcLogP, TPSA, and Rule-of-Five violations; and provides a molecule editor that enables design iterations among other features.

This week, the American Society for Cell Biology, Glencoe Software, and the Open Microscopy Environment launched The Cell, a database of images, videos, and animations of cells from a variety of organisms.

According to the developers, the database is based on Bio-Formats and OMERO which are designed to read and interpret scientific image data and metadata from multiple sources, and enable annotation, visualization. and sharing of image data.

Geneious Pro 5.3 is now available from Biomatters.

Features in this release include compatibility with Geneious Server, the ability to fine-tune any imported reference assemblies, reduced memory usage when importing large contigs and alignments, and GFF 3.0 import and handling, among other features.

SoftGenetics has launched the latest version of its Mutation Surveyor software, which is used for DNA variant analysis of Sanger sequence reads.

The newest release includes two algorithms that reduce false positive mutation calls in regions of poor dye mobility and utilize “seed” sequences within each trace to complete the alignment faster. Also included in the release is a function that recognizes dye blobs and the ability to label, color‐code, and export variants among other features.

Mutation Surveyor has been validated for use in clinical sequence analysis by the UK's National Genetics Reference Laboratories and UPMC, a health system affiliated with the University of Pittsburgh. The software is compatible with the output files of several capillary electrophoresis systems including the ABI Prism, Beckman Coulter CEQ, and MegaBACE platforms.

GraphMLReader v0.11, a Cytoscape plugin for reading and writing basic GraphML files, is available here.

Included in this release is the ability to import basic information such as network and attributes from GraphML files as well as to drag and drop imports from the filer or file links in the browser, among other features.

The European Nucleotide Archive announced this week that EMBL-Bank Release 106 is now available via the European Bioinformatics Institute's ftp servers and other verified mirror sites.

Full release notes are available here and here.

Version 1.9 of the open source software UGENE has been released.

This release includes support for "cloning in silico" and a query designer that lets users analyze signals in the DNA sequence using simple rules to set constraints for algorithms as well as support for high-performance computing and general-purpose computing on graphics processing units.

The University of California, San Francisco, has released Chimera v 1.5, an extensible program for interactive visualization and analysis of molecular structures and related data.

New features in this release include Ramachandran plots, a graphical interface to the Modeller program for homology modeling, metal ion coordination analysis, Segger tools for electron microscopy and tomography, and calculation of theoretical SAXS profiles.

The Scan

Study Links Genetic Risk for ADHD With Alzheimer's Disease

A higher polygenic risk score for attention-deficit/hyperactivity disorder is also linked to cognitive decline and Alzheimer's disease, a new study in Molecular Psychiatry finds.

Study Offers Insights Into Role of Structural Variants in Cancer

A new study in Nature using cell lines shows that structural variants can enable oncogene activation.

Computer Model Uses Genetics, Health Data to Predict Mental Disorders

A new model in JAMA Psychiatry finds combining genetic and health record data can predict a mental disorder diagnosis before one is made clinically.

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.