CH*4550 / MBG*4350
Fall 2004
Bioinformatics Assignment
DUE: 4:30 pm, Wednesday, October 6th, 2004
Instructions:
Answer the following questions using a word processing program. You will need to be able to insert
graphics that you obtain from the internet. Your answers must be submitted electronically in the form
of a Word, Wordperfect, or .pdf-format file.
Submission: email to jdawso01@uoguelph.ca
File Formats: Word, Wordperfect, .pdf (preferred)
Lay out: 1 1/2 spacing, 1 inch margins all around.
Font: Times New Roman, 12-point
Title page: with title of assignment, name, date submitted
LATE POLICY:
-10% / day, up to –50%. NO CREDIT after 5 days late.
• A resubmission will be required if any deviation from these criteria occurs,
resulting in penalties if the resubmission is handed in late.
THE INVOLVEMENT OF MASPIN IN BREAST CANCER DEVELOPMENT.
1 mark
1 mark
3 marks
1 mark
1 mark
PUBMED searching
Briefly answer the following questions based on a search of the PUBMED database. Be sure
to include the full reference(s) you use to formulate any responses.
1. a) How many research articles from 1998 to today deal with maspin and breast
cancer?
b) Of these, how many are classified as review articles?
2. Using the reference list obtained in question 1 above, explain the relationship between
maspin and breast cancer development.
Sequence Database searching.
3. Beginning with the nucleotide search webpage at pubmed
(www.ncbi.nlm.nih.gov/entrez), locate the nucleotide record for the human maspin
mRNA sequence.
a) What is the accession code for the record?
b) Click on the link to the record, and list the official name given to the gene
1 mark
4. At the top right of the nucleotide record webpage is a link labeled “Links”. Within
that drop-down link, access the Gene webpage for human maspin. Display here the
data generated on that webpage.
2 marks
5. Click to enter the Entrez Gene webpage for maspin. Locate and display the protein
sequence for maspin in FASTA format by accessing the drop-down menu for the
coding region of the gene. Keep this sequence handy for questions and 7 and 11.
CH*4550 / MBG*4350
Fall 2004
6. Click on the homology Map Viewer link within the human maspin Gene webpage to
display the chromosome locations of homologous maspin genes in the rat and mouse.
1 mark
a) What kind of homologs are these genes?
2 marks
4 marks
1 mark
b) On which chromosome is the maspin gene located in each of these organisms?
BLAST Searching
7. Perform a BLAST search on the human maspin from question 5 above and determine
the percentage of amino acids that are identical and conserved (“positive”) in the rat
and mouse sequences.
CLUSTALW Sequence Alignment.
8. Display the 5’-untranslated region of the human maspin gene.
2 marks
9. Using any search engine you prefer, find and display the consensus DNA sequence for
optimal binding by the p53 tumour suppressor protein and list the source from which
you obtained this information.
4 marks
10. Using the CLUSTALW alignment website found at
www.ch.embnet.org/software/ClustalW.html, identify the best p53 binding site in the
human maspin gene 5’ untranslated region. Display the output of your searches.
5 marks
1 mark
3 marks
3 marks
3 marks
______
40
marks
Secondary Structure Prediction Tools at ca.expasy.org
11. Use the HNN, GOR and SOPMA tools from ca.expasy.org to predict the secondary
structure of the human maspin protein, using its primary sequence from question 5
above. Align the predictions with the sequence and display as a single alignment.
Tertiary Structure Prediction at ca.expasy.org
12. With the SWISS-MODEL three dimensional model prediction website accessible
through the ca.expasy.rog website, use the first approach mode to produce a homology
model of maspin. This will require that you be emailed with the results of the
modeling.
a) Which protein with a known three dimensional structure has the lowest
probability that the sequence is similar by chance (P(N))?
b) Display a picture of your three dimensional model of maspin (you will need to
use a program like DeepView or Rasmol to view and save pictures.)
c) Access the pdb file that came with your predicted model using a word
processing program. Find the secondary structure prediction for maspin
within at pdf file. Now add this information as a fourth line to your secondary
structural predictions and display this information.
d) How well do the secondary and tertiary structural predictions agree? Discuss
any major disagreements between the two methods.
CH*4550 / MBG*4350
Fall 2004
Bonus Question.
You are grading reports from a 1st year food science course on the history of ice cream. The
grading sheet indicates that the introduction is to be marked out of 10 marks, with 3 marks for
grammar and spelling, 3 marks for style, and 1 mark each for including:
• Marco Polo
• Catherine de’Medici
• Charles I
2 marks
• Emporer Nero.
What grade would you give to the following introduction and why?
We don’t know who invented ice cream for sure. One story goes that Marco
Polo saw ice cream in China and brought it back to Italy. The myth continues
with the Italian chefs of the you Catherine de'Medici taking this magical dish
to France when she went there in 1533 to marry the Duc d'Orleans, with
Charles I rewarding his own ice-cream maker with a lifetime pension on
condition that he did not divulge his secret recipe to anyone, thereby keeping
ice cream as a royal perogative.