In Genome Biology this week, scientists at Maine's Jackson Lab have launched the MouseCyc database. The curated database houses metabolic pathway data for the lab mouse and has been integrated with genetic and genomic data from the Mouse Genome Informatics database and pathway information from other organisms, says the abstract.
New programs have come out as well. One, called Ibis, is a new, "accurate, fast and easy-to-use" base caller for Illumina's Genome Analyzer. Max Planck Institute for Evolutionary Anthropology researchers say that it reduces error rates and increases the number of usable reads. Ibis is freely available here. Another, called Synorth, also online, can be used "for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes," developers say.
A study led by the University of California, Berkeley's Jillian Banfield and the University of Michigan, Ann Arbor's Gregory Dick looked for genome signatures in metagenomic datasets. Shared nucleotide sequences can help classify metagenomic sequence fragments, and in this work, the scientists analyzed metagenomic sequence data from two acidophilic biofilm communities. Genome signatures revealed previously unknown low-abundance organisms and a putative plasmid, they say.
Finally, a study takes a genome-wide look at how two DNA/RNA binding proteins regulate gene expression. Using high-throughput gene expression profiling, researchers in Madrid found that in cells depleted of TIA-1 (T-cell intracellular antigen-1) and TIAR/TIAL1 (TIA-1 related/like protein), the genes expressed are involved in controlling inflammation, cell-cell signaling, immune-suppression, angiogenesis, metabolism, and cell proliferation.