Tag Archives: dark matter

Tip of the Week: Functional Abundance Profile Searching in Genomes

Wow, how can you resist blogging about an article who’s title begins “Dissecting biological ‘‘dark matter’’…”? I found the article while working on a new ‘sponsored’ (read ‘free’) tutorial on the Integrated Microbial Genomes with Microbiome Samples (or IMG/M) resource. (I’m hoping the tutorial will be released in the near future & I’ll post when it is available.) IMG/M is a microbial resource that specializes in the analysis of metagenomes. Metagenomes are becoming hot – we’ve blogged about them in the past, as have lots of others. According to the article I found, “biological dark matter” refers to our paltry knowledge & understanding of the Earth’s microbial diversity. The article reports a method for isolating individual bacterial cells from the microbiome of the human mouth, but for my contribution to understanding microbial diversity, I want to give you a tip on using the IMG/M resource to select protein families in genomes based on their relative abundance. Click the image above to view the tip, or follow the links in this post to learn more on your own.
ResearchBlogging.orgMarcy, Y., Ouverney, C., Bik, E.M., Losekann, T., Ivanova, N., Martin, H.G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D.A., Quake, S.R. (2007). Inaugural Article: Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences, 104(29), 11889-11894. DOI: 10.1073/pnas.0704662104

http://img.jgi.doe.gov/cgi-bin/m/main.cgi