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Chemical Computing, Gene Codes, Sapio Sciences, Ensembl, The National Center for Biotechnology Information, Symyx

Chemical Computing Group has released the 2007.09 version of the Molecular Operating Environment (MOE) for the Solaris10 Operating System from Sun Microsystems, running on UltraSPARC and x86 architectures.

Gene Codes has released Sequencher 4.8, its enhanced software program for DNA sequence assembly and analysis on PCs and Macs.
Sequencher 4.8 adds the Translated Variance Table, which helps researchers find DNA sequence variations that alter protein coding. Other features include four new reporting formats for saving or presenting results along with supporting data. For more information on these and additional new features, or to download a demo visit

Sapio Sciences has released a copy number variation analysis tool to support Illumina’s Infinium arrays.
The Exemplar Analytics 4.0.8 tool will provide CNV analysis and include the following features: support of all Illumina DNA analysis beadchips from the Human-1 to Human1M Beadchip; principal components’ analysis for admixture corrections; allele counting of hemizygous SNPs; and an update of the annotations database with current information from dBSNP, Entrez Gene and Gene Ontology.

The Wellcome Trust Sanger Institute and European Bioinformatics Institute have released Version 47 of Ensembl with additional and upgraded features such as new mouse 37 assembly and genebuild, New Human genebuild, and resequencing data from Craig Venter’s and Jim Watson’s genomes.
Ensembl 47 includes WormBase 180 (Caenorhabditis elegans) and several variation updates including Homo sapiens, Mus musculus, Rattus norvegicus, Ornithorhynchus anatinus).
The new human database consists of additional SNPs/genotype data from Venter’s and Watson’s genomes; added genotype data for dbSNP; and added Affymetrix genome-wide human SNP Array 6 data.
The new mouse database includes SNPs/genotypes from Sanger mouse strains, mapping old dbSNPs to a new assembly.

The National Center for Biotechnology Information has released dbSNP build 128, which includes Homo sapiens; Ovis aries, Glycine max, and gorilla genomes. 

Symyx will now provide researchers with ACD data via the Internet using a dedicated XML-based web service called the Symyx ACD Web Service.
The service is accessed via a former MDL chemical directory, now called the Symyx Available Chemicals Directory, a structure-searchable collection of commercially available chemicals, with the option of accessing up-to-date ACD data using a dedicated XML-based Web Service.

The Symyx ACD Web Service was developed with design input from a global pharmaceutical R&D organization seeking business process efficiencies and a simplified mechanism for distributing dynamically-updated chemical sourcing data to globally dispersed project teams, the company said.

Filed under

The Scan

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.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.