Finally, NCBI Genomes recognises Archaea*

I’ve been complaining about this for years. They fixed it. The NCBI have reorganised their genomes FTP site and finally, Archaea are not lumped in with Bacteria.

GenBank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/
RefSeq:  ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/

Archaea are still included in the ASSEMBLY_BACTERIA directory; hopefully that’s next on the list.

[*] to be fair, they’ve always recognised Archaea – just not in a form that makes downloads convenient

Snippets: guts, cancers, statistics

File under “interesting articles that I don’t have time to write about at length.”

  • Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents
  • Long ago, before metagenomics and NGS, I did a little work on detection of Archaea in human microbiomes. There’s a blog post in the pipeline about that but until then, enjoy this article in PLoS ONE.

  • Mutational heterogeneity in cancer and the search for new cancer-associated genes
  • This article is getting a lot of attention on Twitter this week. Brief summary: cancer cells are really messed up in all sorts of ways, most of which are not causal with respect to the cancer. Anyone who has ever looked at microarray data knows that it’s not uncommon for 50% or more of genes to show differential expression in a cancer/normal comparison, so this is hardly a new concept. I think we need to move away from ever-more detailed characterizations of the ways in which cancer cells are “messed up.” We know that they are and that doesn’t provide much insight, in my opinion.

  • The vast majority of statistical analysis is not performed by statisticians
  • Interesting post by Jeff Leek, summarized very well by its title. It points out that many more people are now interested in data analysis, many of them are not trained professionally as statisticians (I’m in this category myself) and we need to recognize and plan for that.

Bonus post doing the rounds of social media: Using Metadata to Find Paul Revere. Social network analysis, 18th-century style. Amusing, informative and topical.

Oops: taxonomy #fail

My journey from bench scientist to bioinformatician began with archaeal genomes. So I was somewhat startled to read The catalytic mechanism for aerobic formation of methane by bacteria, in which we learn about the “ocean-dwelling bacterium Nitrosopumilus maritimus“.

So was Jonathan Eisen of course and you should go and read why. Every top hit in a Web search for that organism tells us that Nitrosopumilus maritimus is an archaeon.

Looking forward to a rapid correction and apology from Nature.

Title edited from “phylogeny” to “taxonomy” at the insistence of @BioinfoTools ;)