PATRIC is a integration portal (as the name implies) of data concerning disease-causing infectious bacteria. Or to put it in their words: PATRIC is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools. [...]
Mike the Mad Biologist points to a nice article that describes aspects of the next-generation sequencing technologies with some helpful animations to illustrate the different styles. Mike goes on to describe that the sequencing itself isn’t the rate limiting step–the assembly and analysis steps are the hurdles really. The dust certainly hasn’t settled on the [...]
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 [...]
Hey, say you’ve got a bacterial genome you just sequenced in your spare time (hey, the way technology is going, it’s not far off) and you need to do a quick and dirty annotation to get you started. Well, there are several tools out there to do that, predict genes, annotate regions, etc. I’d like [...]
This week’s tip introduces a nice feature and tool of the Viral Bioinformatics Resource Center (VBRC). There are a lot of great tools at the VBRC to search and analyze hundreds of viral genomes. Most, if not all, of the tools can be used for searching and analyzing bacterial genomes also. The tool we are [...]
UCSC 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 [...]
I’m currently at the third annual JGI Users Meeting titled Genomics of Energy and Environment. The first workshop is about IMG and when it finishes I’ll update you on anything new or interesting. A later session is on Biomass Feedstocks (for energy production), so look in this post for updates on that to. I’ll be [...]
Came across a nice bacterial genome browser today via “Discovering Biology in a Digital World:” the Genome Projector. The is a map of over 100 bacterial genomes including a circular genome map, a genome map, a pathways map and a “DNAWalk” map. Put in a search term (I put “iron” in here, you know, as [...]
Recently I was watching a show about the beginning of life on Earth, and they were talking about how important Cyanobacteria was for making oxygen available for other life forms. As they talked about astrobiology and the search for other inhabitable planets, it occurred to me that I know a way of searching for microbes associated [...]
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