Category Archives: Research

In the previous post I described a method for efficiently blasting a medium-large dataset (33 million sequences).  One down side to using blast on a dataset this size is the very large size of the output xml file, in this … Continue reading →

The blast algorithm is, with good reason, one of the most widely used tools in bioinformatics.  It allows a reasonably quick comparison between a set of sequences and a (potentially very large) database or set of sequences in a fasta … Continue reading →

We just published the first analysis of a microbial community inhabiting natural frost flowers in the journal Environmental Microbiology Reports.  Our results are a bit surprising, and I’ll get to them shortly.  First, a brief look at what we did.  … Continue reading →

In an earlier post I mentioned some odd microbiological observations that our group made during field work in Barrow, AK in 2010.  I also talked about how I’m hoping to repeat that observation this year, using the microscopy technique FISH.  … Continue reading →

The last couple of posts on this blog have been about 16S gene sequences, and how microbial ecologists use these sequences to identify different bacteria and determine evolutionary relationships.  The primary method for the latter is to build phylogenetic trees.  … Continue reading →

***NOTE*** For the code in this article to work you must use the reverse complement of the probe, not the probe itself.  I’ll correct it in the near future. ************ I’m preparing for some spring field work in Barrow, Alaska … Continue reading →

Sort of.  Over the last three years I’ve  been fortunate to participate in a working group on the origin of life, coordinated by John Baross.  John is the only faculty member in the group, the rest are graduate students from … Continue reading →

I’m continuing the theme of cost-saving lab tricks (see this post on the topic).  Over the summer my laptop died on me.  While putting everything back together I couldn’t find my key for the commercial synchronization software (Allway Sync) that … Continue reading →

Many thanks to Robert Krulwich, co host of NPR’s RadioLab, for a great article on frost flowers.  Reading through the comments I can see that there is a lot of public interest in this phenomenon.  I want to take the … Continue reading →

I have an experiment that I want to do that involves growing bacteria in relatively large volumes (around 10 L) in a cold room for several weeks.  Typically in this sort of experiment you stir the cultures with a magnetic … Continue reading →