NCBI

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, ... Read more

You might think the coolest thing about the Next Generation DNA Sequencing technologies is that we can use them to sequence long-dead mammoths, entire populations of microbes, or bits of bone from Neanderthals.


... Read more

No more delays! BLAST away!

Time to blast. Let's see what it means for sequences to be similar. 

First, we'll plan our experiment.  When I think about digital biology experiments, I organize the steps in the following way: 

           A.  Defining the question

B.  Making the data sets

           C.  Analyzing the data sets

D.  Interpreting the results

I'm going intersperse my results with a few instructions so you can ... Read more

We'll have a blast, I promise! But there's one little thing we need to discuss first...

I want to explain why I'm going to use nucleotide sequences for the blast search. (I used protein the other day). It's not just because someone told me too, there is a solid rational reason for this.

The reason is the redundancy in the genetic code.

Okay, that probably didn't make any sense to those of you who didn't already know the answer. Here it is. ... 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 ... Read more

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 perhaps you're wondering just what kind of information is stored for different kinds of records and if you could search for this information.

I wrote a book that covered this topic quite thoroughly, a couple of years ago, for the NCBI structure ... 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 from the ... 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. Serendipity strikes when we Blink ... 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