Content Related to blast

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 ...

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 ...

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. Human insulin, colored by rainbow. Image from the Molecule World iPad app by Digital World Biology. I wanted to find ...

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.

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 ...

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 ...

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 ...

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: Cannibals, Killer Viruses, and Other Journeys to the Edge of Science but I ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many ...

In which we identify unknown human proteins. 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 ...

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 ...

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 ...