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
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?
BLAST for beginners
This tutorial is designed as a quick introduction to the BLAST family of sequence analysis programs.
These slides show a progression of steps in using blastn, beginning at the home page for the National Center for Biotechnology Information (NCBI) ( www.ncbi.nlm.nih.gov ) and ending at PubMed , a tool for searching scientific literature. In this series, you will see how to submit a nucleotide sequence, compare it to ... Read more
BLAST for beginners introduces students to blastn, a commonly used tool for comparing nucleotide sequences (DNA and RNA). This popular tutorial shows how to do a blast search with a nucleotide sequence, highlights information in the search results, and shows how to interpret the E value and alignment scores. 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
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
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.
some years back by Richard Preston. (I guess he has a new book, too, ...