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Downloads & Upgrades: Mar 19, 2010


CLC Bio has released a whole-genome de novo assembler that it said will assemble genomes "of any size," including human and plant genomes, on a single workstation.

The company said that the assembler also offers a graphical user interface that allows molecular biologists to easily set up, adjust, and run their large genome de novo assemblies.

Compared to other de novo assembly software, which CLC said requires more than 300 GB of RAM for large genome assemblies, the company's assembler "can assemble the same datasets on a single workstation computer with only 48 GB of RAM."

The company said that the assembler is also up to 50 times faster than existing packages and that it can mix datasets from different sequencing technologies, including Illumina, SOLiD, Roche 454, Helicos, and Sanger sequencing instruments.

Release 103 of the EMBL Nucleotide Sequence Database is available from the European Bioinformatics Institute FTP site as well as the US mirror site and other mirrors.

The release contains more than 185 billion sequence entries comprising 281 trillion nucleotides. Files total 133 GB compressed and 963 GB uncompressed.

Accelrys has launched Discovery Studio 2.5.5, which includes new protein-modeling algorithms, access to the latest version of the Cambridge Crystallographic Data Center's GOLD docking program, and improved usability and performance.

The release includes a new 3D quantitative structure-activity relationship method, a protocol for calculating residue electrostatic energy for predicting protein stability and thermostability, two new user interface "discovery guides," and 64-bit server compatibility.

Version 32 of the Reactome Knowledgebase is available here.

The latest version of the curated resources includes a new topic on the role of the CDO cell-surface protein in myogenesis, as well as several revised and updated topics.

RefSeq 40 is available via FTP here.

Release 40 includes 13,853,798 records, 9,856,489 proteins, and sequences from 10,291 different organisms.

The Scan

Wolf Howl Responses Offer Look at Vocal Behavior-Related Selection in Dogs

In dozens of domestic dogs listening to wolf vocalizations, researchers in Communication Biology see responses varying with age, sex, reproductive status, and a breed's evolutionary distance from wolves.

Facial Imaging-Based Genetic Diagnoses Appears to Get Boost With Three-Dimensional Approach

With data for more than 1,900 individuals affected by a range of genetic conditions, researchers compared facial phenotype-based diagnoses informed by 2D or 3D images in the European Journal of Human Genetics.

Survey Suggests Multigene Cancer Panel VUS Reporting May Vary Across Genetic Counselors

Investigators surveyed dozens of genetic counselors working in clinical or laboratory settings, uncovering attitudes around VUS reporting after multigene cancer panel testing in the Journal of Genetic Counseling.

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.