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This Week in Nucleic Acids Research: Oct 29, 2014

A Chinese team introduces MethBank, a database integrating genome-wide methylation information gleaned from single-base resolution sequencing data — including information on mouse and zebrafish samples sequenced at different stages of development. The database is designed to bring together data on methylation and gene expression profiles, the study's authors say, as well as genetic variants, differentially methylated parts of the genome, and sites containing frequently methylated cytosine and guanine bases. "Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different development stages," the study's authors write, "and accordingly providing an important resource for the epigenetic and developmental studies."

Researchers from the French National Institute of Agronomic Research, the University of Glasgow, and elsewhere present a database describing biochemical pathways and networks in the protozoan parasite Trypanosoma brucei, the culprit behind African trypanosomiasis or sleeping sickness. After sequencing and annotating the T. brucei genome, the team set to work outlining the parasite's metabolic patterns in the database, dubbed TrypanoCyc, during a two-day "jamboree" initiative. Through community participation and curation in the subsequent years, the database has come to house information on T. brucei metabolic networks under a variety of conditions.

Members of the Mouse Genome Database (MGD) Group outline features of MGD, a central repository designed to integrate genomic, genetic, and biological information on laboratory mouse strains. In addition to a mouse gene directory, for instance, the MGD contains a catalog of non-coding genomic elements such as functional RNA, quantitative trait loci, and sites in the genome with ties to mouse phenotypes, including phenotypes that may offer clues to human conditions. In particular, authors of the paper highlight an MGD feature called the Human-Mouse: Disease Connection, a feature added to the database to facilitate interactions between human and mouse genes, physical features, and disease traits.