Sometimes when you go digging through the databases, you find unexpected things.
When I was researching the previous posts on insulin structure and insulin evolution, I found something curious indeed.
In my last post, I wrote about insulin and interesting features of the insulin structure. Some of the things I learned were really surprising. For example, I was surprised to learn how similar pig and human insulin are. I hadn't considered this before, but this made me wonder about the human insulin we used to give to one of our cats. How do cat and human insulin compare?
It turns out, that all ... Read more
Yesterday, I wrote about using the BLOSUM 62 matrix to calculate a score for matches between two proteins. Those scores give us a good start on understanding how blastp determines whether two sequences are matching by chance or because they're more likely to be related. But that's not all there is to calculating a blast score, and there's at least one other statistic to consider as well, the E value.
It all ... Read more
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.
Introduction Once you're acquainted with proteins, amino acids, and the kinds of bonds that hold proteins together, we can talk about using this information to evaluate the similarity between protein sequences. We can easily imagine that if two protein sequences are identical, then those proteins would have the same kind of activity. But what about proteins that are similar in some regions, and not others, or proteins that only ... Read more
Let's play anomaly!
Most of this week, I've written about the fun time I had playing around with NCBI's Blink database and finding evidence that at least one mosquito, Aedes aegypti, seems to have been infected at some point with a plant paramyxovirus and that the paramyxovirus left one of its genes behind, stuck in the mosquito genome.
During this process, I realized that the method I used works with other viruses, too. I tried it with a few random viruses and sure enough, I found some interesting things.
You've got a week to give it a try. Let's see ... Read more
Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank
This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things.
In this last part, I discuss a general method for finding novel things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students.
I. The back story ... Read more
Part IV. Assembling the details and making the case for a novel paramyxovirus
This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.
Part III. Serendipity strikes when we Blink
In which we find an unexpected result when we Blink while looking at the mumps polymerase.
This is the third in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes. And yes, this is where the discovery happens.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. ... Read more
Part II. What do mumps proteins do? And how do we find out?
This is the second in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes, and a general method for finding interesting things.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. ... Read more
Part I. The back story from the genome record
Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. ... Read more
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