Create cladograms that depict evolutionary relationships.
Analyze biological data with sophisticated bioinformatics online tool.
Use cladograms and bioinformatics tools to ask other questions and to test the ability to apply concepts relation to genetics and evolution.
Part 1 Procedures:
Read the information on p. S44 and form an initial hypothesis to where the fossil specimen should be placed on the cladogram based on observations made earlier in the pre-lab activity. Draw the hypothesis on a cladogram like in figure 4 in the lab manual.
Under "Upload Search Strategy," click "Browse" & locate one of the files you downloaded.
Click "View."
A screen will appear with parameters for query already configured. DO NOT alter any parameters!
Click "BLAST" at bottom of screen when ready.
Collect data and analyze it for that particular gene:
The 1st section is a graphical display of the matching sequences.
The 2nd section "sequences producing significant alignments" shows species with identical genes sequences. Things to note:
As you move down the list, they become less common.
The most similar will be listed 1st.
Click on a species to get a full gene report on the sequence, scheme, & research journal on it.
Click "distance tree of results" to see a cladogram with species having a similar sequence to gene placed on the cladogram according to how closely their gene matched.
Answer the "Analyzing Results" questions for that gene and redraw your cladogram (if needed).
Repeat steps 3 & 4 for all genes downloaded. Make sure to create a FINAL cladogram after the 4th gene has been analyzed.
Answer the evaluating results questions.
Part 2 Procedures: Design your own
Go to the Entrez Gene website and search for your desired gene. Ideas are listed on p. S50 in addition to whatever you would like to search.
Click 1st link & scroll down to "NCBI Reference Sequences" (RefSeq)
Under "mRNA & Proteins" click the 1st file name.
Just below the gene title, click on "FASTA."
The nucleotide sequence will be displayed.
Copy the entire gene sequence then go to BLAST homepage as in part 1.
Click "nucleotide BLAST."
Paste sequence into "Enter query sequence" box.
Give query a title if need/want to save it & work on it later.
Under "Choose Search Set," select if want to search human genome only, mouse genome only, or all available.
Under "Program selection," choose if want highly similar or somewhat similar sequences.
Click "BLAST."
Answer analysis questions.
Things to note in this lab:
Make sure you answer the questions for each section of the lab (if called for).
This is a live website. It may work super quick, it may take long time. It all depends on who is accessing the website at the same time as us.
If you want to see how I set up my notebook for data / observations, please ask me.
This is an individual lab! You are not working with your classmates!
The website changes from time to time. Buttons may get moved around, links may not work, etc. Everything is still there, you just have to look.