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Downloads & Upgrades: Jul 23, 2010


Golden Helix has launched SNP & Variation Suite (SVS) 7. The company said that the latest version of the genetic analysis tool suite includes a new genome browser that allows users to compare their results with other sources, such as the Database of Genomic Variants or the University of California, Santa Cruz, Genome Browser.

SVS 7 also offers the ability to analyze non-human genomes, including mouse, rat, chicken, cattle, horse, rice, and soy. The software also supports the direct import of data from NimbleGen’s comparative genomic hybridization arrays and AffymetrixCytogenetics Whole-Genome 2.7M and Molecular Inversion Probe arrays.

RefSeq 42 is now available via FTP from the National Center for Biotechnology Information .

The release includes genomic, transcript, and protein data available as of July 13 and includes 15,038,858 records, 10,640,515 proteins, and sequences from 10,728 different organisms.

Two Fold Software has launched Qualoupe LIMS, a laboratory information management system with "an intuitive, configurable user interface designed to enhance the user experience and revolutionize workflow."

The company said that the Qualoupe user interface is icon-driven and follows a "Just Enough Information Model" that requires minimal mouse clicks to operate. The interface also monitors data that is commonly used by each user in order to speed the selection of records.

The developers of the Bowtie short-read aligner have released Crossbow 1.0.4 and Myrna 1.0.4.

Crossbow is a software pipeline for whole-genome resequencing analysis. It combines Bowtie, SoapSNP, and a genotyping tool in an automated parallel pipeline that runs on the Amazon cloud. The new version has been rewritten as an Amazon Elastic MapReduce application as opposed to an Elastic Compute Cloud application, which provides a friendlier user interface for monitoring and manipulating jobs, according to the developers.

Crossbow 1.0.4 also offers separate cloud, Hadoop, and single-computer operating modes.

Myrna is a cloud-computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short-read alignment and Bioconductor for interval calculations, normalization, and statistical testing. Myrna 1.0.4 includes a web-based graphical user interface for composing and submitting Myrna Elastic MapReduce jobs and other improvements.

MolPort, an online chemical marketplace, said this week that it has added its structural data to the publicly available PubChem database and that all the data it has provided is linked to its compound-procurement module.

"While PubChem lists some commercial sources for chemical compounds, it is primarily a research, not an ordering tool," the company said in a statement, adding that it views its resources as "a bridge between PubChem and chemical suppliers."

MolPort said that compounds from multiple suppliers can be obtained with a single order and invoice through its website.

The Scan

Fertility Fraud Found

Consumer genetic testing has uncovered cases of fertility fraud that are leading to lawsuits, according to USA Today.

Ties Between Vigorous Exercise, ALS in Genetically At-Risk People

Regular strenuous exercise could contribute to motor neuron disease development among those already at genetic risk, Sky News reports.

Test Warning

The Guardian writes that the US regulators have warned against using a rapid COVID-19 test that is a key part of mass testing in the UK.

Science Papers Examine Feedback Mechanism Affecting Xist, Continuous Health Monitoring for Precision Medicine

In Science this week: analysis of cis confinement of the X-inactive specific transcript, and more.