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Proteome BioKnowledge Library, AFCS-Nature Molecule Pages, SCOP, Ensembl 19, Bioconductor, and VEGA 1.5.1

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Incyte is offering free access to HIV- and AIDS-related data in its Proteome BioKnowledge Library during December as part of its monthly Disease Spotlight program. The HIV and AIDS Disease Spotlight provides 25 protein reports related to HIV and AIDS with curated annotations based on relevant publications. The data is available at www.incyte.com/diseaseview.


The Nature Publishing Group and the Alliance for Cellular Signaling have launched the AfCS-Nature Molecule Pages, a database of curated information about more than 3,000 proteins involved in cellular signaling. The pages, available at http://www.signaling-gateway.org/molecule/, are a step toward the goal of creating a complete computer simulation of cellular behavior, according to the AfCS.


A new SCOP (structural classification of proteins) release (1.65) is available at http://scop.mrc-lmb.cam.ac.uk/scop/. The new version contains 20,619 PDB entries and 54,745 domains.


Ensembl 19 is available at http://www.ensembl.org/. New data includes an updated gene build for the NCBI 34 assembly, including 200-300 improved predictions produced as a result of corrections in the gene building soft-ware. The build contains 23,531 gene predictions with 31,609 transcripts.


A Bioconductor package using John Storey’s Q-value code [BioInform 08-04-03] is available at http://www.bioconductor.org/repository/devel/package/html/qvalue.html


VEGA 1.5.1, a program to convert, manage, and visualize 3D structures, is available from Milan’s Istituto di Chimica Farmaceutica e Tossicologica at http://www.ddl.unimi.it/. New functions include the capability to add hydrogen molecules; and RMSD cal-culation and Accelrys archive file (.arc) support in the trajectory analysis.

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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.