Author Archives: Jeff
Mega megablast – conducting a massively parallel blast
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
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At first look at the microbiology of frost flowers
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
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The UAF sea ice course returns!
Another great opportunity was announced at UAF, which seems to be full of them these days. This is the return of the UAF sea ice course, last taught in 2008. Here’s the announcement: ******************************* This spring (May 8-18), UAF is … Continue reading
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Metagenomic Assembly
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
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Place it!
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
Going FISHing
***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
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A new model for the origin of life
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
RIP Carl Woese!
Sunday marked the passing of Carl Woese, one of the most important figures in microbial ecology in recent decades. In fact that’s a bit of an understatement, his discoveries and the methods he pioneered have profoundly altered our understanding of … Continue reading
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On academia
I don’t ordinarily post job listings on this blog, but this is a great opportunity for a talented student interested in environmental microbiology. Don’t be thrown off by the location, Fairbanks is a top notch school with a world class … Continue reading
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A better backup
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
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