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Downloads and Upgrades: BioJava 3.0.7, PathSeq Virome, Discovery Studio 4.0, and more

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BioJava 3.0.7 is available here.

Features in this release include a basic genbank parser, added support to parse mmcif records for organism and expression system, and many small bug fixes and improvements.


PathGen Dx has added the PathSeq Virome application to BaseSpace Apps, Illumina's cloud-based informatics application store.

According to the PathGen, the new app lets researchers identify viral genomes that are present in the MiSeq of HiSeq2500 sequencing results. The app filters sequencing data, matches it to a virus database, runs quality controls to remove false positives, and generates a PDF report of genomes in the database that most closely match viral sequences present in the sequenced sample. Currently, PathSeq Virome can identify all known viruses that infect humans in human-derived samples but does not yet support analysis of animal-derived samples.


Accelrys has released version 4.0 of Discovery Studio

This version of the tool includes tools that let users identify mutation sites for disulfide bridges, as well as improvements in both scalability and performance in long-duration simulations among other updates.


Dotmatics has integrated Vortex, its data analysis and visualization solution with Thomson Reuters' Cortellis.

The integration means that scientists can now use Vortex to directly retrieve drug, patent and market information from Cortellis and combine it with their own in-house records.


The genome browser group at the University of California, Santa Cruz has released a new browser for the American alligator Alligator mississippiensis

Bulk downloads of the sequence and annotation data may be obtained from the genome browser ftp server or the downloads page.


SoftGenetics has released a new version of NextGene, its next generation sequence analysis software.

This version of the software includes optimized analysis algorithms, new tools for copy number variation detection, advanced reporting features including target region coverage curves and statistics, and the ability to create a fully automated pipeline that includes the analysis of raw data or BAM files and the ability to upload data to the Geneticist Assistant NGS interpretive workbench.


The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.