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Blast, Rosetta Resolver, Modiro, BioPathwise DM, EMBOSS 4.1.0, Customer Hub

The National Center for Biotechnology Information is seeking comments on a new Blast interface design that it is beta-testing here. Improvements include a “Recent Results” feature, which provides links to recent Blast results, and “Saved Strategies,” which allows users to save Blast forms with their parameters and use them later.
NCBI has also released its annotation of the zebrafish genome assembly, build 2.1, which is available through Map Viewer or via ftp, as well as its annotation of the gray short-tailed opossum genome assembly, build 2.1, through Map Viewer or ftp.

Rosetta Biosoftware has released version 7.0 of its Rosetta Resolver gene expression data analysis system, which supports the Clinical Data Interchange Standards Consortium's SEND (Standard for Exchange of Non-clinical Data) format as well as additional gene expression platforms, such as the Illumina platform.

Protagen has launched Modiro, a proteomics software package that automates the identification of post-translational modifications by analyzing thousands of mass spectrometry profiles in parallel to identify unknown mass shifts, sequence errors, and unspecific enzymatic cleavage of amino acids. Modiro is compatible with “all leading” mass spectrometers, the company said. The program was developed as part of a collaboration with Bruker Daltonik.

The BioAnalytics Group said that it plans to release BioPathwise DM, a server-based data-management system, in late March. The system enables groups of researchers to “document, store, and share data along with any reports, records, peer reviewed journals, or other relevant information,” the company said in a statement. The initial release will include modules for qPCR data and image data.

EMBOSS 4.1.0 is available here. The release includes two new applications (edialign and wordfinder), improvements for other applications, and several bugfixes. A version for Microsoft Windows is available here.

InforSense has launched Customer Hub, an online resource for its customers to share best practices and collaborate. Customer Hub, available here, includes more than 100 ready-to-use applications, tutorials, and templates for the company’s KDE workflow platform.

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The Scan

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.

Seagull Microbiome Altered by Microplastic Exposure

The overall diversity and the composition at gut microbiome sites appear to coincide with microplastic exposure and ingestion in two wild bird species, according to a new Nature Ecology and Evolution study.

Study Traces Bladder Cancer Risk Contributors in Organ Transplant Recipients

In eLife, genome and transcriptome sequencing reveal mutation signatures, recurrent somatic mutations, and risky virus sequences in bladder cancers occurring in transplant recipients.

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.