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Cognia, Molecular Mining, DNAstar, Ensembl, SCOP, ASTRAL

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New York-based Cognia has launched Cognia Molecular, an information management system for entering, organizing, and utilizing biological and chemical information. The system provides annotation clients, a relational database, and search and visualization interfaces that allow researchers to create and customize databases for analyzing their proprietary information in the context of the scientific literature.

Molecular Mining of Cambridge, Mass., has released GeneLinker Gold version 3.0 and GeneLinker Platinum version 2.0. The latest versions of the company’s expression analysis software offer several usability enhancements, including linked visualizations and the ability to launch Spotfire DecisionSite products from within the programs. Analytical improvements include improved data import from a wider variety of microarray platforms, an F-test ANOVA procedure to test for differentially expressed genes between two or more experimental conditions, and Lowess normalization for two-color microarray data.

DNAstar has released its GenVision genomic data visualization and publication software. GenVision creates PostScript images from annotation data stored in text format to visualize genomic data as both circular and linear maps. The software is available as a plug-in for Adobe Illustrator for Mac and Windows and as a standalone version for Windows. DNAstar has also updated its Lasergene sequence analysis software suite to include enhanced data for locating potential transcription factor binding sites in nucleotide sequences.

Version 9 of Ensembl is now available at www.ensembl.org. The new release is built upon an overhauled API and schema, according to its developers, and offers improved consistency over previous versions. Most data remains unchanged, but has been imported into the new schema. One exception is SNP data, which now uses dbSNP 107. SNP data are now available for human, mouse, and mosquito.

A new SCOP (structural classification of proteins) release (1.61) is available at http://scop.mrc-lmb.cam.ac.uk/scop/. The new version contains 17,406 PDB entries, 28 literature references, and 44,327 domains. The associated release 1.61 of ASTRAL, a collection of databases and tools for analyzing protein structures and sequences derived from SCOP, is available at http://astral.stanford.edu.

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The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.