1. Lab 3 – BLAST – Directed
It’s a BLAST!
(too easy?)

2. What do you mean by “directed?”
Just to be clear, this is a modified version of Lab 3 in your manuals.
However, you’ll still need the original lab manual for consultation and questions to answer.
Yes?

3. What do you mean by “BLAST?”
BLAST stands for Basic Local Alignment Search Tool and is hosted on the NIH’s website.
The NIH are the National Institutes of Health – a governmental biological science agency made of a lot of different branches and locations.
BLAST allows you to input a sequence of either DNA nucleotides or amino acids for comparison to a database of known sequences.
Think of this like a DNA/protein fingerprint database.
The best part? You don’t need a complete sequence to use it, hence the term “local alignment.”

4. What’s a BLAST search like?
Using BLAST is like if I gave you a phrase of three words and asked you to search every book in the library for it.
Including similar words.
Including misspellings.
Including the words separately.
Including any other partial matches.
And you have to do it in seconds.
In a weird way it’s like Shazam or Soundhound.

5. How do we do this lab?
The directions are pretty straightforward this time and don’t need much explanation, but here’s the overall goal/sequence:
Try to place a fossil within an existing cladogram.
Download four sequences of DNA nucleotides.
Imagine you’ve sequenced these in a lab.
Upload the four sequences to the BLAST database.
Identify the proteins associated with the sequences.
Research the function of the protein.
Modify the existing cladogram based on your findings.

6. What do BLAST results look like?
BLAST is going to give you a lot of information.
This same database is used by Ph.D. researchers in the same way you’ll be using it, after all.
You’ll first get a big list of matches ranked in order of closest match, with the highest “score” at the top.
Of most concern to you is the following info:
Organism name.
Given as binomial Latin name.
Protein made by the gene.
Given right after the organism name.
Who else makes it.
Found in the “Distance Tree” results.
These are your clues.

7. What else? There’s a weird internet security thing going on.
CB will not permit me to host the DNA sequences locally unless I compress them to one folder.
To complicate matters, you are also blocked from downloading the sequences via the website listed in the lab.
So, use my website (Labs section) to download the files as one folder.
At home, you can use either website (my site or the College Board’s blog site).
Either way, note that the sequences are not readable by your computer.
Just download them locally, then upload them to BLAST. You don’t ever need to actually open them.

8. What else?
This is a standard informal lab report and questions to be answered are specified in the instructions, including in the background.
Note: You should still write a hypothesis.
Your hypothesis is your guess for where the fossil shown in your manual fits in the given cladogram based on morphology.
There are a few preliminary things to do as well, prior to starting the main part of the lab (just to get your brains a-workin’).
Defining vocabulary (introduction), practicing making cladograms (background information), and a sample analysis.
For the record, they’re designed for a wide age range and are probably toward the easier side for you. They’re still well done.

9. Distance Tree Tips Refer to this slide when needed
When you go to the Distance Tree of Results view, your sequence will be labeled as “unknown” and highlighted in yellow.
To make things easier to view:
Right-click anywhere in the distance tree window and select Layout > Slanted Cladogram.
Right-click again and select Expand All.
At the top of the window, click Tools > Edit Labels and select Common Name.
Use the slider along the top of the window to zoom in. Click and drag to move the window to the lower right.
And there are the close relatives!

10. Uh, go? Get two computers for your table.
Remember, read the packet. It tells you what to do and when to refer to the lab manual.
And when not to.
Also, don’t get bogged down in vocabulary.
Consider just leaving space for it and doing it later.
You won’t be able to do this whole lab in class. Which part would you rather do at home? DNA analysis or definitions?