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Bioinformatics

Category archives for Bioinformatics

This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. UPDATE: I’m not so certain anymore that the strains are the same. I’m doing some work with nucleic acid…

I was pretty impressed to find the swine flu genome sequences, from the cases in California and Texas, already for viewing at the NCBI. You can get them and work them, too. It’s pretty easy. Tomorrow, we’ll align sequences and make trees. Activity 3: Getting the swine flu sequence data

I’m a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases. In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I’m a little skeptical about the blowfly, but… Now, you might wonder,…

Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let’s do a bit of digital biology and see what we can learn. Activity 1. What kinds of animals get the flu?

A couple of years ago, I answered a reader’s question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and the reported coverage to estimate…

In which we identify unknown human proteins.

In which we search for Elvis, using blastp, and find out how old we would have to be to see Elvis in a Las Vegas club.

“Digital biology,” as I use the phrase, refers to the idea of using digital information for doing biology. This digital information comes from multiple sources such as DNA sequences, protein sequences, DNA hybridization, molecular structures, analytical chemistry, biomarkers, images, GIS, and more. We obtain this information either from experiments or from a wide variety of…

A friend of mine; serial entrepreneur, and former president of Genetic Systems; Joe Ashley, told me once that starting a business is an unnatural act. Now that I’ve done it, I agree. Even with my multiple back-up plans, possible grants, and part-time activities, my stomach still hurts and my mind is racing. My new company…

Have you ever wondered how to find things in the NCBI databases? Maybe you tried to find something but didn’t know how it was spelled. Or maybe you tried to use a common name like “pig” or “deer” to find information in a database, not knowing that all the organism names are in Latin. Or…