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Downloads and Upgrades: Oct 14, 2011

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The Bio-Soft team at the University of Chicago has released RaptorX, a protein structure modeling web server.

According to the developers, the tool is good at modeling protein sequences that lack close homologs in the Protein Data Bank.


The genome browser team at the University of California, Santa Cruz, has released an updated browser for Saccharomyces cerevisiae.

The updated browser includes several new chromosomes for yeast from the Saccharomyces Genome Database project.


This week, Elsevier launched the Protein Interaction Browser, a new application available on its SciVerse platform that allows readers to explore protein-protein interaction networks for proteins in scientific papers.


This week, Agilent released version 2.0 of its CytoGenomics software.

The latest version of the tool supports comparative genomic hybridization and SNP-based analysis of genetically complex samples such as hematological cancer samples.


Definiens has released an updated version of its Quantitative Digital Pathology Portfolio.

The release offers updated versions of Definiens Tissue Studio and Definiens Developer XD, and adds a new component called Definiens Image Miner that integrates data mining with image analysis for biomarker-based research.


Real Time Genomics has released RTG Investigator version 2.3.

The software supports data from multiple sequence platforms, provides error-tolerant read mapping and alignment, and offers Bayesian SNP/indel variant calling among other capabilities.


A beta version of BASE 3.0 is available for download here.

The beta contains new functionality needed to support sequencing experiments with expression-like data, but may require bug fixes, according to its developers.


This week, OpGen launched Genome-Builder, a software module that provides capabilities for precision sequence assembly.

According to the developers, the tool provides a high-resolution, ordered visual map of genomic architecture that enables the detection of structural rearrangements at 10 times the resolution of traditional cytogenetic techniques.


The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

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.