BLAST LAB
PREP
IF YOU DO NOT COMPLETE THIS PRELAB AND COME CLUELESS TO CLASS YOU WILL FAIL THIS LAB.
1) Read background on page S41 an summarize it.
2) Read the rest of the instructions for the lab S41-S50.
3) Complete Prelab Activities (including Online Activities)
4) Watch these videos:
http://www.youtube.com/watch?v=HXEpBnUbAMo
http://www.howcast.com/videos/359904-How-To-Use-NCBI
Additional videos can be found by searching “NCBI BLAST” on YouTube.
5) Review this tutorial document:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs
1. Navigate to NCBI and the BLAST page as usual.
2. At the top, click “Help” to go to the BLAST Documentation Page.
3. Under the heading “About BLAST,” there is a handbook that has both
6) Download the files attached to this homework and have it on a pin drive to save time in class
You can also play around in BLAST ahead of time if you want, as well.
REQUIREMENTS
Pre-Lab (Due: 11/14/13 - Stop By)
1) Background summary
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Do online activities [Practice Only. No Work Due]
2) Questions and activities in Instruction Manual before actual investigation
Part A) Investigating Fossil (Due: 11/15/13 @ Class End)
1) Hypothesis: Make a prediction based on fossil bone structure / morphology as to where in the tree fossil would be
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Do Lab (See Procedures in Instructions Manual)  Run BLAST of Genes 1-4 [To Do. No Actual Proof Required]
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Analyze results of Blasts collectively. [To Do]
Hints:
o Consider ALL blasts in your decision
o Scores are important for comparing organisms in each genes, but you cannot compare them across genes because of
different gene lengths
o % Query is useful to see if size of gene is similar
o % Identical is useful to decide degree of similarity overall
o E value is statistical test. Remember anything less than 1e-4 means enough similarity to imply homology. This is the
most important piece of data.
o It is interesting to look at actual query between organisms and see alignment of base pairs (Remember lines means same
base, blanks means significant mutation, and + means insignificant mutation that does not alter protein much), however
it is not very useful for the purpose of this lab. More interesting here is the actual # of bases in common or gaps, etc.. But
all of that is already computed by the % Identical and E values scores. So do not spend too much time on that.
o Look at names of proteins and research their function. Do you best to understand funciton. Then, in each blast to try to
understand why fossil would have it.
o Look at names of organism with homology in each blast and research them.
o Think about why homologies would exist for those organisms for that gene
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Think about why the fossil would have all of the 4 proteins and why it would be similar/homologous to all those
organisms. Then do your best to piece it together and make a decision about your hypothesis.
The book also has insight on how to use probability rules to put information of many genes together.
You definitely want to look at taxonomy and tree views to gain insight into classification and phylogeny as seen in each
gene (show up in all trees and how closely they show in general)
Put all above hints together. Look at scores, look at function, look at organisms with homology, look at
taxonomy/phylogeny, think about the step where you considered function and homology together. Then make a decision
2) Results: Present supporting evidence from blast analysis to support your analysis statement. Enough evidence considering all
hints above and all blasts should be included. I will not give you a good grade if your evidence points are not convincing. There
are no right answers per say. There sure is, but what I am mostly looking for is your reasoning.
3) Analysis Statement: Results rejected hypothesis that.... OR Results failed to reject hypothesis that...
4) Conclusion: Write about what you learned with this lab and answer all the analysis questions from the instructions Manual
Part B) Individual Exploration (Due: Before winter break)
1) Choose an enzyme/protein from the list or some other enzyme of interest (Do some research into some interesting and famous
biology proteins). Email Mr. Lima or talk to him to make sure it is has not been selected already.
2) Use BLAST to analyze enzyme genome (nucleotide blast and protein blast if both available).
3) Use BLAST / Internet Resources to answer all suggested questions in the Instructions Manual
4) Come up with 3 additional questions that blast could help you answer.
Note: As it was with Part A, for each question, your work should be tied in to BLAST somehow. If possible / applicable with data,
analysis, and hypothesis.