Lab 3: BLAST
Objectives:
Objectives:
- 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:
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.
- Locate & download gene files. Found on AP Bio Investigative Labs Page.
- Upload gene sequence into BLAST.
- Go to BLAST home page.
- Click "Saved Strategies" in the top right menu.
- 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
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:
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.