Shotgun sequencing. Sounds like fun. Speculations on the origin of the phrase I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage, transduce E. coli, and hope for the best. Consistent with the shotgun metaphor, we even used to store our microfuge tubes in plastic bullet boxes that my boss found at the sporting goods store. (Apparently this practice was unique ... Read more

Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes, 2145 viruses, and genome sequences from ... Read more
Note to self: doing live BLAST searches during a lecture is not a good idea. Would Julia Child make her viewers watch the food bake? Standing in front of a class and waiting for results to appear, makes me realize how much instructors can learn a lot from watching Julia Child demonstrate cooking. I think if Julia Child taught bioinformatics this is how she would discuss BLAST results with her class: Afer a BLAST search has been submitted to the NCBI, your results are stored there for 24 hours, and you can get them with the request ID. If you do ... Read more
About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught. I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question: How do you sequence a genome? Before we get into the technical details, there are some other genomic questions that you might like answered. How much does it cost to sequence a genome? I remember in 2002, when we were at the ... Read more
In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted:
I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it would never get done.
Well, okay, technically speaking he didn't ask me for help. But, since I'm a ... Read more
The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses. Why not use the Web? Before going on, I should probably explain, why we use desktop programs, we have so many things available on the web. We do use the web whenever we can. Web services are nice because you can shift the computation burden to someone ... Read more
I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too happy about it, though. By this time of the school year, they've caught on that every snowday has a price. And, they will pay ... Read more
There's nothing like the first day of class to make you appreciate the difference between the equipment you end up using at schools and the equipment that you get to use on the job. For the month of January, I'm teaching a night class in bioinformatics at a local community college. We're introducing lots of web-based programs, and databases, and concentrating on the sorts of activities that biotechnology technicians are likely to use on the job. It's fun. It's practical. And I don't have to suffer through any lectures about the Semantic Web. I'm also getting reminded (although not ... Read more
Our goal for this course (BioSci256) is to introduce you to some of the tools and databases that are widely-used in bioinformatics and give you lots of hands-on practice in using these tools to look at some questions in biology. Since many of you are either studying biotechnology or working in a health-related field, we will focus quite a bit on practical applications. I posted tonight's topics here since I've been told that some of you might not have access to Blackboard for a couple of days. Feel free to look around the place. ScienceBloggers ... Read more
When computers first entered the mainstream, it was common to hear them getting blamed for everything. Did you miss a bank statement? that darned computer! Miss a phone call? - again the computer! The latest issue of Science had a new twist on this old story. Now, instead of a researcher failing to take responsibility for doing sloppy science, we're back to blaming the computer. Never mind that the lab was using home made software that they "inherited from someone" (and apparently didn't test it) the five retracted papers were the fault of the software! Not the ... Read more

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