blast

Sandra Porter, Austin Community College and Digital World Biology LLC, Seattle, WA

Our bioinformatics course at Austin Community College focuses on basic concepts and techniques.  Students learn how to search databases, use molecular models, apply sequence analysis tools, and characterize genetic variation.  Although bioinformatics provides us with interesting real-life examples to study, our abilities are limited when it comes to finding student projects that include opportunities to make new discoveries.  We don’t have a lab and we’re not able to generate our own data, so we rely ... Read more

For many years, many of you have been using our popular BLAST for beginners tutorial and the BLASTing through the kingdom of life activity. We decided with the recent updates to the NCBI BLAST pages that it was a good time to update the tutorial and some of the sequences as well.  In the tutorial, we've added images that represent the current web pages at the NCBI.  For our data set of sequences, we made a couple of the sequences longer, to remove the ambiguity in determining which sequence matches the query best.  

Of course, this meant that we also needed to update the answer key ... Read more

by Sandra Porter


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 vertebrates produce ... 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

Ebola virus has impressed me as creepy ever since I read "The Hot Zone: A Terrifying True Story some years back by Richard Preston. (I guess he has a new book, too, Panic in Level 4 ... 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 ... Read more

yep, I've become a videoblogger, at least sometimes.

See the first video below. Be kind in the comments, this is a new thing for me.

This video introduces the different blast programs, discusses word size, and how blastn works, the blastn score and the E value. The treatment is light and not too in depth, but as I said, it's an introduction.

... Read more

In which we're reminded that database searches are experiments, too.

One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes even a day later, is a different database. And, if you query a different database, you may get a different result.

The series that I'm currently posting is one that I started working on a couple of ... Read more

Last year I wrote about an experiment where I compared a human mitochondrial DNA sequence to primate sequences in the GenBank. Since I wanted to know about the differences between humans, gorillas, and chimps, I used the Entrez query 'Great Apes' to limit my search to a set of sequences in the PopSet database that contained gorillas, bonobos, chimps, and human DNA.

A week ago, I tried to repeat this experiment and...

It didn't work.

All I saw were human mitochondrial sequences.  I ... Read more