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GeneSifter Core Edition, XP Glide, UniProt 2.0, ADME/tox databases, Smack 1.0, UCSC Genome Browser, Ensembl, EMBOSS 2.9.0

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VizX Labs has released GeneSifter Core Edition — a new version of the company’s microarray analysis system designed for core facilities. Core Edition adds administrative tools that allow core facilities to provide and manage GeneSifter accounts for their clients, the company said. Computing and storage resources are provided via off-site secure servers and the facility staff can assign these resources to multiple user accounts.


Schrödinger has released a new version of its XP (extra-precision) Glide docking software that includes a new sampling algorithm and scoring function to improve docking accuracy by eliminating false positives. Further information is available at: http://www.schrodinger.com/Support/ftpupdate.html.


UniProt 2.0 is now available from the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, and the Protein Information Resource at http://www.pir.uniprot.org/. The release contains 1,487,788 entries (153,871 from UniProt/SwissProt, and 1,333,917 from UniProt/Trembl).


Bio-Rad’s informatics division has released thirteen new ADME/tox databases. The databases include data related to the blood brain barrier, human intestinal absorption, log D, log P, mutagenicity, plasma-protein binding, and water solubility.


OpenEye Scientific Software has released Smack 1.0, which converts substructure and reaction queries expressed in MDL file formats to Daylight’s Smarts strings.


Concurrent with the release of the draft assembly of the dog (Canis familiaris) genome last week, the University of California Santa Cruz genome bioinformatics group has released a Genome Browser and Blat server, as well as dog sequence and annotation data at http://hgdownload.cse.ucsc.edu/downloads.html#dog. Ensembl has also released a preliminary assembly of the dog genome at http://pre.ensembl.org/Canis_familiaris. The sequence for the dog genome is based on 7.6X coverage and contains around 2.5 billion base pairs.


EMBOSS 2.9.0 is available at http://emboss.sf.net. New features include modifications to ACD and the libraries as part of the development of an EMBOSS ontology. In addition, Embassy packages can now be compiled and linked against an installed version of EMBOSS.

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The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

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.