Using BLAST
There are quite a few sites offering BLAST services scattered across the Internet. There are also different implementations of the BLAST algorithm (e.g. NCBI BLAST2 and WU-BLAST).
The Usage of these sites varies a bit between them. However the basic interpretation of the results is the same and is usually the main source of confusion or problems for most people.
We will use the the NCBI BLAST server. The server is perhaps the most user friendly, has lots of colours and added extras. The downside is that is can be very slow, especially in the afternoon. Faster versions can be found at the EBI and at ExPASy (and Newcastle soon!).
This exercise has two parts. Firstly, we will work through some BLAST tutorials. Then we will progress on to a small exercise using BLAST to analyse an unknown protein sequence.
How does BLAST work? – click here for a good description from Peking Univerisity.
BLAST TUTORIALS
In this section I’m going to cheat a bit. There are a number of excellent BLAST tutorials already on the web so we’ll run through a couple of these.
Step 1: Firstly we’ll look at a tutorial at Seattle Central Community College. This is a very simple introduction to using BLAST at NCBI.
Go through the tutorial, clicking on the green arrow to progress through the slides.
Run the tutorial by clicking here.
Step 2: A more complex, but excellent tutorial is available online at NCBI. Take some time to run through the tutorial at the NCBI site (Just do the BLAST tutorial for now - not the PSI-BLAST tutorial) and then return back to this page.
Click here to start the NCBI BLAST tutorial.
More detail on BLAST searching is also available from the BLAST guide at NCBI by clicking here.
More information about BLAST (frequently asked questions) is available here.
Now that you have an idea about how do a BLAST search go on to the next part in which we will use BLAST to look for sequences that are similar to a mystery sequence.