BLAST  Project (40 pts) - due Oct. 11th

Assignments:  In addition to writing on exams and homework, there will be two special assignments.    

To earn an excellent grade on your report, you must:

·                     communicate clearly;   make it interesting and informative to the reader; 

·                     answer all listed questions, with your thinking clearly explained;

·                     turn the report in on time (late penalty - 3 pts/ first day + 2 pts/additional day; no credit after 10 days)

·                      format for your reports:

o         Place your name, UTeID, class, date, seq #, 20-mer seq., name of protein, complete FASTA seq. properly formatted, etc.  information on the cover page

o        use one and one-half spacing for the body of your text

o        use single spacing for figure captions and references

o        references: include at least 4 primary references (see below) in J Biol Chem style - place a number within the text (1) and then provide a list of references at the end, single spaced.  e.g., Borst, P., and Elferink, R. O. (2002) Annu. Rev. Biochem. 71, 537?592 .

o        make sure that Figures included have a figure legend and Tables have a title or heading 

              be neat, with few or no spelling or grammatical errors.

Assignment 1. You will be assigned a 20-amino acid sequence from the list below.  Each sequence is a fragment of an actual protein.  Use your sequence to do the following steps and then answer the questions below for your report:  

(a) Do a first BLAST run using your 20 a.a. sequence.  What is your protein? What is the complete amino acid sequence of the protein?  

(b) Now using the entire a.a. sequence, do a second BLAST run to find related sequences.  Carefully select a subset of the related sequences and do a Multiple Sequence Alignment using a program like CLUSTAL W.   Choose related proteins from at least five to eight other diverse organisms, if possible.  Using relatively diverse organisms (archaeal, bacterial, and eukaryotic) will make it easier to identify the most conserved amino acids within the protein.   Prepare a figure or table showing a sequence alignment of your protein and identify the conserved amino acids.  

(c)  Which amino acids (be specific, aa #) do you think are most important for preserving the structure of the protein?  Why?  Which amino acids do you think are most important for the function of the protein?  Why?   

(d) You should find that a structure is known for your protein.  What is the PDB code?

(e)  Using PyMOL (or a similiar program) make an original figure illustrating your protein.  There are links to tutorials on using PyMol on the links page (e,g, Tyler's PyMol How To demo slides)

(f)  In approximately one-half page, briefly describe the function of your protein.  

REPORT / Grading - 40 pts total:      For an example of a past report - click BLAST

1) Cover page - your name, the date and class, your sequence number and given 20 a.a. sequence, the name and source of your protein and the complete protein sequence in FASTA format -  5 pts

3)  Table showing your multiple sequence alignment using 5 selected BLAST hits - 15 pts, 

4) Original PyMOL or similar figure - 10 pts, and

5) Half-page functional summary of your protein - 10 pts.  Tell a clear, story with a  minimum of typos / errors and include four (4) primary references to go with your report (see above).

Regarding plagiarism:  Please be aware that plagiarism is considered to be ethically unacceptable. Here is a one suggestion as to how to avoid plagiarism: While reading the sources of information that you plan to use in preparing your assignment, take notes on the content, using your own words.  While preparing your paper, refer to your notes, rather than the original source.  If you feel the need to use a phrase from a source, be sure to put the phrase in quotes, and reference the source.  In these days of the internet, it is very easy to find material that can be easily be plagiarized. Be warned, however, that the existence of the internet makes it much easier than ever before to detect plagiarism.  If you plagiarize in writing assignments, you run a high risk of getting caught, and a high risk of failing the course.

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Select your 20 amino acid sequence for the first writing assignment by the day of your birth from the list below  (e.g. if you were born on September  11, 2001 - your sequence is VNFKIRHNIE DGSVQLADHY: 

             Sequences for CH370  2012  -  BLAST Writing Assignment  

 1) VGKKREFVER LTSVAAEIYG

 2) GQGLQEGERD FGVKARSILC

 3) NLSRLQEAGE LLRTEINRSV

 4) FAYHEMMTHV PMTVSKEPKN

 5) SSMGHDGVVD EQSGKIVNDL

 6) LLDIGGGFPG SEDTKLKFEE

 7) AASPLEKVCL VGCGFSTGYG

 8) PLLKFDLFYG RTDAQIKSLL

 9) QNFYEKIYNA LKPNGYCVAQ

10) YDNGWNYEIY VKNDNTIDYR

11) FDSNEAMYTK IKQGGTTYDI

12) RTFAKNGGCC GGNGNNPNCC

13) HQLKNNPSSR RHITMLWNPD

14) VIVEETPPER WFVGGRSVAE

15) LGCYTESGQA IPVSFNGVKG

16) SADYVMVSAS LGVLQSDLIQ

17) LDTMVAALSC CQEAYGVSVI

18) VIFGNRQADR SPCGTGTSAK

19) TEGVYKVSWT EPTGTDVSLN

20) EEQLRADHVF ICFPKNREDR

21) ATATMGYKHK ALDANEAKDQ

22) CFYKLLTGAL ERDCGISPDD

23) QNRSYSKLLC GLLAERLRIS

24) GFEIVRPGHP LVPKRPDACF

25) FTEEEFKRLN INAAKSSFLP

26) VEYMEEEKKT WGTVFKTLKS

27) AVSDARCVFD MATEVGFSMH

28) REAEADASEG ADMLMVKPGL

29) FRGFGGPQAL FIAENWMSEV

30) AARDKLETMT PNVKAIVGDE

31) LGKKNRSLNG EKVDQVDYLL

Every sequence should have a perfect match with a real protein, but that protein may not have a structure that has been determined.  However, if that is the case you should be able to find a closely related protein that does have a structure available.