Teaching with the new BLAST

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Sandra Porter

BLAST is a collection of programs that are used to compare sequences (DNA, RNA, or protein) to larger collections of sequences that are stored in databases. I've used BLAST as a teaching tool for many years, partly because it's become a standard tool for biological work and partly because it's very good at illustrating evolutionary relationships on a molecular level.

A few months ago, the NCBI changed the web interface for doing BLAST searches at their site. I wrote earlier about changes that I made to our animated tutorial in response to the new BLAST. Now, I want to mention some of the good and bad things about the change in design.

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What I like about the new interface:
If you make yourself an account at the NCBI, your searches and results are now saved for 48 hours and available from links in a table when you log in. I really like this feature! We do a similar thing in our Finch software and I've always liked being able to store sets of results and work with them later.

Having your results stored in a database is really helpful when you want to do lots of searches with different parameters and compare the results. It's also convenient when you want to do the Julia Child thing. You can set up lots of searches ahead of time and your results will be stored at the NCBI and ready for your discussion.

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This is a nice improvement. In the past, the NCBI only saved the search results for 24 hours and you had to keep track of the request ID. The new options are much nicer. I also like knowing the expiration time and having the option to save strategies that worked well.

What I don't like
1. If you're teaching and demonstrating live BLAST searches in front of a class, be sure to log out first! When you have your own account, all the parameters you use get stored and are presented on the input form as the default choices. If you forget this, you will automatically be using different parameters and databases for searching than your students.

This can lead to some very weird experiences that make your search results different from those of your students and make it challenging to figure out what's happening - especially in the middle of a lecture. To quote Charlie Brown: "AAARGH!"

So, if you're going to do a live search, log out first and save yourself the grief.

2. The other thing is that you must look at your results to see what you really did. I expected that checking an option in the web form would override other parameters, but it's not clear that it really happens.

Here's an example:

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I thought that clicking this check box would change the search parameters to match the ones that we used to use for looking at primer binding sites.

No. In fact, I'm not sure how this option changed the search.

Fortunately, you can see which parameters blast used by scrolling down to the very bottom of your search results and seeing what they were.

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You can't get all the information here. Nothing seems to record whether you used any kinds of filters - (low complexity, repeats, etc.) or not. You'll have to go back to the original web form to get that information. Still, you can find out quite a bit.

That's all for now. It's time for me to blast off.