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Downloads and Upgrades: BioCyc 16.5, inForm, MacVector 12.7, and more


BioCyc 16.5 is available here.

This release includes updates to the BioCyc website, including new additions to the EcoCyc and MetaCyc databases, downloadable data files, and a downloadable Pathway Tools software/database bundle.

Golden Helix has released a new RNA-seq analysis package for its SNP & Variation Suite toolkit.

This latest addition provides capabilities for RNA sequence data quality assurance, analysis, and visualization.

Genes & Genomics has launched a cloud-based Next Generation Sequence data analysis service.

The company analyzes genome, exome, transcriptome, and metagenomics data and offers de novo assembly services. It also provides customers with data storage and management facilities.

PerkinElmer has released a new version of inForm, its software product for automated image analysis in oncology studies.

The software is available in two packages: inForm Tissue Finder and inForm Cell Analysis.

Tissue Finder helps users find relationships between multiplexed markers in disease studies. It is also used for high-throughput imaging when extracting proteomic and morphometric information from intact tissue sections. It relies on a patented algorithm that automates the analysis of images of tissue samples and provides improved accuracy in scoring and quantifying biomarker expression levels in tissues.

The inForm Cell Analysis software is designed for pathologists and oncologists who want the power of inForm Tissue Finder, but require lower throughput.

MacVector has released version 12.7 of its MacVector software, which provides tools for sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and other functions.

The release includes a new Cloning Clipboard tool that simplifies the creation of new DNA constructs and lets users join molecules together in a drag-and-drop interface. The tool designs and documents all subcloning operations from simple digests to complex multi-fragment procedures. It also annotates sequences with the history of every ligation event, showing the enzymes used, the date, and any end modifications. Other updates include performance enhancements to the Dot Plot tool and the Align To Reference editor.

A new release of UniProt GO Annotation, a project run by the UniProt group that provides assignments of gene products to the Gene Ontology, is available via ftp.

The Genome Browser group at the University of California, Santa Cruz, has released a new genes track for the mouse genome browser.

The new release has 59,121 transcripts, compared with 55,419 in the previous version. Also, the total number of canonical genes has increased from 28,661 to 31,227.

Instem has released a new version of OmniViz, its data mining and visual analytics solution.

Version 6.1 includes support for Windows 7 32-bit and 64-bit operating systems, and offers access to more memory for processing large datasets.

SoftGenetics has released a new version of its NextGENe software.

The release includes a new module for copy number variation analysis, customized reporting capabilities, and other improvements.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.