Tag Archives: archaea

Tip of the Week: Genomic Encyclopedia of Bacteria & Archaea (GEBA)


Being summer, a strangely slow connection and some other factors, I am embedding a talk from Doug Ramsey (posted on SciVee) on the GEBA project at JGI (instead of doing a tip myself :). The GEBA project recognizes that many, if not most, of the bacterial and archaeal genomes that have been sequenced to date have some relevance to human disease or other human interest. This of course is reasonable, but it also leads to big gaps in our knowledge of bacterial evolution and genomics, knowledge that would help us better understand those genomes that we find relevant and knowledge that in and of itself can be quite interesting and potentially useful. View the talk to learn more about this project to sequence 100 phylogenetically diverse bacterial and Archaeal genomes.
I’m also posting this as an introduction to JGI’s Adopt a Genome project. This project allows student groups to adopt and study a bacteria in the GEBA project and hopefully add to our knowledge and annotations of the genome while learning. The students can then annotate the adopted genome by using IMG-ACT.

Archaeal Genome Browser from UCSC

Archaeal Genome Browser from UCSCUCSC announced the Archaeal Genome Browser created by the Lowe Lab at UCSC last week. The browser has been accessible for a while, but this is the public ‘unveiling’ and announcement. The interface and use is very similar to the UCSC Genome Browser (free tutorial), though of course modified and geared to the analysis of Archaeal genomes. So add another resource and database to your toolbox, it looks like another good and useful one. As the announcement says:

Currently there are more than 50 completed archaeal genomes, the least studied domain of life. Although archaea and bacteria are both prokaryotes, often co-existing in the same environments, many aspects of archaeal cell biology such as DNA replication, repair, transcription, and translation are homologous to those found in eukaryotes. Some members of archaea are also notable for inhabiting extreme environments, including boiling terrestrial hot springs, black smoker vents at the bottom of the ocean, the ultra briny water of the Dead Sea, and highly acidic drainage water from ore mines, to name a few.