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Downloads & Upgrades: Jun 25, 2010

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Version 33 of the Reactome Knowledgebase is available here.

The new release includes a new topic, chromosome maintenance. Topics with new or revised information include axon guidance, synaptic transmission, transmembrane transport of small molecules, metabolism of proteins, diabetes pathways, signaling in the immune system, and signaling by GPCR.


GenBank 178.0 is available via ftp from the National Center for Biotechnology Information.

Release 178.0 comprises approximately 116 gigabases and 120 million entries from non-WGS, non-CON sequences, and 168 gigabases and 58 million entries from WGS sequences.

Uncompressed, release 178.0 flat files require roughly 444 gigabytes for sequence files only. The ASN.1 data require approximately 364 gigabytes.


Symyx Technologies has released the Symyx Direct 7.0 data cartridge, a system for registering, searching, and retrieving chemical and biological entities stored in relational databases.

Symyx Direct 7.0 supports natural post-translational modifications and custom modifications, the company said. It also includes a new, hybrid representation "that combines the best features of bioinformatics and cheminformatics notations."


SeqMonk v0.10.0, a software tool for visualizing and anaylyzing high-throughput mapped sequence data, is available here.

New features include directional quantitation probes, support for either removing duplicate reads upon import or ignoring them in every quantitation method, the ability to extend reads when importing them to facilitate the analysis of single-end ChIP-seq data, and the ability to update genome annotation sets when new annotations become available.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.