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Downloads and Upgrades: Jun 3, 2011


The Center for Bioinformatics and Computational Biology at the University of Maryland has released TopHat 1.3.0.

The new version of the spliced read mapper for RNA-seq data includes a restructured internal workflow that compresses all temporary data during a run in order to improve running time on networked filesystems.

The software now supports both GTF2 and GFF3 formats and can take gzip or bzip2 compressed FASTQ or FASTA files as input

Japan's Riken has released a new web service interface, called Semantic-JSON, to provide investigators with access to life science research data across multiple public and private domains.

The interface accesses a "virtual laboratory cloud center" named the Scientists' Networking System, which brings together 192 public database projects and provides access to data records and a network of semantic relationships.

The tool lets users access data from across the SciNetS network using the programming languages and information tools they normally use in their research by defining a set of simple but relevant commands for accessing and searching SciNetS data and their semantic relationships and delivering results in the JavaScript Object Notation format.

A paper describing the tools was published in a recent issue of Nucleic Acids Research.

The Scan

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.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.