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BioTools, Bioperl, EBI, Cray, PerkinElmer


BioTools of Edmonton, Canada, has released GeneTool 2.0. The updated DNA analysis software now offers a vector construction tool that can be used to run virtual cloning experiments; improved multiple alignment capabilities to align sequences up to thousands of kilobases in length; restriction enzyme and translation viewing options; the ability to export images in a number of formats; a new DNA dot plot tool; and a 3D DNA structure viewer.

Bioperl 1.1.1, a developer’s release, is available at: DIST/bioperl-1.1.1.tar.gz or The release is intended to provide a preview of the next stable series, Bioperl 1.2, which is expected to be available before the end of the year. According to the Bioperl developers, many of the features of the 1.2 stable release series are available in 1.1.1, including ontology support, OMIM parsing and support for phenotypes, and support for the new Entrez web programmable resources.

BioLayout Java v1.0b, a tool for visualizing protein-protein interaction networks and protein sequence similarity graphs, is available from Christos Ouzounis’ group at the EBI at: cgg/services/layout. The BioLayout developers recommend running the application on a “fast machine” (at least 1.0 GHz with 250 MB RAM) because large graphs may require a lot of processing and memory.

Cray has shipped five early-production units of the new Cray X1 system, which it is calling “the world’s most powerful supercomputer product,” to five undisclosed customer sites. The X1 product, which the company expects to find use in the life science market, will be formally announced later this year.

PerkinElmer intends to launch its Integrated Microarray Laboratory at the Chips to Hits meeting in Philadelphia next week. The package is based on the company’s ArrayInformatics gene expression software system, but includes new features that streamline the capture of data from the company’s spotters and scanners, according to PerkinElmer.

Filed under

The Scan

Review of Approval Process

Stat News reports the Department for Health and Human Services' Office of the Inspector General is to investigate FDA's approval of Biogen's Alzheimer's disease drug.

Not Quite Right

A new analysis has found hundreds of studies with incorrect nucleotide sequences reported in their methods, according to Nature News.

CRISPR and mRNA Together

Time magazine reports on the use of mRNA to deliver CRISPR machinery.

Nature Papers Present Smartphone Platform for DNA Diagnosis of Malaria, Mouse Lines for Epigenomic Editing

In Nature this week: a low-cost tool to detect infectious diseases like malaria, and more.