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Downloads and Upgrades: SMRT Analysis 1.3.3; AIS ClearCompute; and more

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Pacific Biosciences has released SMRT Analysis 1.3.3, an update of the software for its Single-Molecule Real Time sequencing system. The release includes expanded capabilities for DNA base modification analysis and de novo genome assembly.

Specifically, it automatically detects common types of bacterial methylation including N6-methyladenine, N4-methylcytosine, and Tet-converted 5-methylcytosine, and performs methyltransferase recognition motif analysis. The release also integrates the Celera Assembler, optimized for PacBio sequence data, to facilitate de novo genome assembly.


American Internet Services has launched AIS ClearCompute, a software-as-a-service platform for life sciences that supports research applications like Blast and Galaxy.


The Broad Institute has released GenePattern 3.4

This release provides access to more than 200 analysis tools for analyzing gene expression, proteomics, and SNP data among other types of information.

Users can run the platform on Amazon’s cloud infrastructure and exchange data between bioinformatics tools via GenomeSpace (BI 7/6/2009 and BI 5/4/2012). It’s also easier to create analytic workflows and incorporate new modules into a GenePattern server as a result of updates to its pipeline and module editors, the developers said. Furthermore, data uploads are much faster because of improvements in the platform’s file transfer capabilities.


The Department of Energy’s Joint Genome Institute has released a fourth version of the Integrated Microbial Genomes system, which serves as a community resource for analyzing and annotating genome and metagenome datasets.

Version 4.0 consolidates the individual microbial genome and metagenome databases in the system. Both programs will retain a publicly accessible portal — IMG for microbial isolates and IMG/M for metagenomes — and a password-protected portal — IMG/ER and IMG/M-ER — for collaborators who aren’t ready to release their data.

IMG currently contains 11,753 total genomes, plasmids and genome fragments; 2,075 metagenome samples; and 2,372 genomes and 804 metagenome samples in IMG/ER and IMG/M-ER, respectively.


The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.