Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST
How can bioinformatics be used as a tool to determine evolutionary relationships andto better understand genetic diseases?
• I will be able to analyze biological data with a sophisticated bioinformatics online tool.
• I will be able to use cladograms and bioinformatics tools to ask other questions of my own.
- I will test my ability to apply concepts I know relating to genetics and evolution.
- Turn in DNA fingerprinting packet
Step 1 Form an initial hypothesis as to where you believe the fossil specimen should be placed on the cladogram based on the morphological observations you made earlier. Draw your hypothesis on Figure 4. (this step should be completed).
find two or three other carbon-based units and draw a picture on a whiteboard of your new cladogram and write your proposed hypothesis.
Complete steps 2-4 in the computer lab -answer (Analyzing results questions)
Recall that species with common ancestry will share similar genes. The more similar genes two species have in common, the more recent their common ancestor and the closer the two species will be located on a cladogram.
As you collect information from BLAST for each of the gene files, you should be thinking about your original hypothesis and whether the data support or cause you to reject your original placement of the fossil species on the cladogram.
For each BLAST query, consider the following:
• The higher the score, the closer the alignment.
• The lower the e value, the closer the alignment.
• Sequences with e values less than 1e-04 (1 x 10-4) can be considered related with an error rate of less than 0.01%.
1. What species in the BLAST result has the most similar gene sequence to the gene of
2. Where is that species located on your cladogram?
3. How similar is that gene sequence?
4. What species has the next most similar gene sequence to the gene of interest?
Based on what you have learned from the sequence analysis and what you know from
the structure, decide where the new fossil species belongs on the cladogram with the
other organisms. If necessary, redraw the cladogram you created before.
Now that you’ve completed this investigation, you should feel more comfortable using BLAST. The next step is to learn how to find and BLAST your own genes of interest.
To locate a gene, you will go to the Entrez Gene website (http://www.ncbi.nlm.nih.gov/gene).
Once you have found the gene on the website, you can copy the gene sequence and input it into a BLAST query.
One student’s starting question: What is the function of actin in humans? Do other organisms have actin? If so, which ones?
1. Go to the Entrez Gene website (http://www.ncbi.nlm.nih.gov/gene) and search
for “human actin.”
2. Click on the first link that appears and scroll down to the section “NCBI Reference
3. Under “mRNA and Proteins,” click on the first file name. It will be named “NM 001100.3” or something similar. These standardized numbers make cataloging sequence files easier. Do not worry about the file number for now.
4. Just below the gene title click on “FASTA.” This is the name for a particular format for displaying sequences.
5. The nucleotide sequence displayed is that of the actin gene in humans.
6. Copy the entire gene sequence, and then go to the BLAST homepage (http://blast.ncbi.nlm.nih.gov/Blast.cgi).
7. Click on “nucleotide blast” under the Basic BLAST menu.
8. Paste the sequence into the box where it says “Enter Query Sequence.”
9. Give the query a title in the box provided if you plan on saving it for later.10. Under “Choose Search Set,” select whether you want to search the human genome only, mouse genome only, or all genomes available.
11. Under “Program Selection,” choose whether or not you want highly similar sequences or somewhat similar sequences. Choosing somewhat similar sequences will provide you with more results.
12. Click BLAST.
Below is a list of some gene suggestions you could investigate using BLAST. As you look at a particular gene, answer the following questions:
• What is the function in humans of the protein produced from that gene?
• Would you expect to find the same protein in other organisms? If so, which ones?
• Is it possible to find the same gene in two different kinds of organisms but not find the protein that is produced from that gene?
• If you found the same gene in all organisms you test, what does this suggest about the evolution of this gene in the history of life on earth?
• Does the use of DNA sequences in the study of evolutionary relationships mean that other characteristics are unimportant in such studies? Explain your answer.
This packet is due tomorrow- (be sure to to the "Getting Started" section on pages 43 and 44).
Attach your hypothesis(es) about the evolution of flight.