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Downloads and Upgrades: UCSC Genome Browser, Bowtie 0.12.9, GenBank 193.0, I2E 4.0, and more


The UCSC Genome Browser group has released four tracks for the human assembly derived from dbSNP 137.

The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the genome browser. One track contains all mappings of reference SNPs to the human assembly while the other three tracks are subsets of this track.

Bowtie version 0.12.9 is now available.

The release fixes a bug as well as a number of errors and warnings from the previous incarnation of the tool.

GenBank 193.0 is now available via ftp from the National Center for Biotechnology Information.

Uncompressed flatfiles for 193.0 require roughly 579 GB for sequence files only or 624 GB to include the short directory, index, and text files. The ASN.1 data require approximately 474 GB.

Relay Technology Management has released the pipeline-to-pathway target searching module for Business Development Live! 1.2, the latest version of the company’s flagship comparative asset and trend analysis software for the life sciences.

BD Live! 1.2 gives biopharmaceutical firms access to a database of company, target, and drug relationships as well as information on industry trends. The module lets these customers run searches based on molecular targets of interest in order to explore the competitive landscape.

Omixon has released a free genome browser for customers of its Omixon Target 1.2.

According to the company, the browser lets users visualize next-generation sequencing and mutation data, particularly in targeted genomic regions.

MacVector released a free version of MacVector 12.7 this week, providing its customers with a free basic edition of its sequence analysis application for Macintosh computers.

MacVector Free includes many of the basic sequence editing, documentation and analysis functions. It lets users download sequences in most sequence formats and save them in any supported format. It also performs simple click cloning operations to generate new constructs and provides access to Entrez and Blast.

Reactome 43 is available here.

Topics with new or revised events include immune system, cell cycle, extracellular matrix organization, metabolism, signal transduction, and gene expression. New pathway illustrations for this release include cell cycle and apoptosis.

Linguamatics has released I2E 4.0, the latest version of its text-mining software platform.

The release includes a new application programming interface for I2E’s web services, improvements to its virtual data integration abilities to help users analyze and extract information from disparate sources, new advanced chemistry capabilities, and a new reporting format for query results.

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.