BCB 444/544 Fall 07
Study Guide Final – Dec 3
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BCB 444/544 - F07
Study Guide Final
For Final Exam (Dec 10)
Answers will be discussed in Review Session on Thurs Dec 6
FINAL EXAM Mon Dec 10 9:45 – 11:45 AM in MBB 1420 & 1340
NOTE CHANGE: ENTIRE FINAL EXAM WILL BE OPEN BOOK/NOTES!!
General Comments:
Final Exam will include 100 pts and contain 2 sections:
1) a 50-minute written Exam, open-book, open-notes, open-computer
20 pts In Class: Comprehensive
40 pts In Class: New material (since Exam 2)
All topics covered in class, lab and assigned readings:
Lectures 27-38, HW5-6, Chps 9-11 & 17-19, Labs 9-11
2) a 50-minute lab practical Exam, open-book, open-notes, using
computers
40 pts In Lab: Practical (Comprehensive)
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Some questions will involve computation; bring your calculators if you like.
All required formulae or tables will be provided.
Some questions will require short essay-like answers that demonstrate
your understanding of key concepts covered in the course.
How to study:
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Review all topics, problems & correct answers included in:
o Study Guides 1 & 2 & 3/Final (this document, see below)
o Exams 1 & 2
o Graded HW Assignments
Review topics on which you missed points or need review in:
o Lecture PPTs (1 - 38) (39 will not be covered)
Spend time reviewing procedures and answers for:
o Lab Exercises (1-11) (Lab 12 will not be covered)
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Study Guide Final – Dec 3
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Hints:
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For comprehensive part of Final Exam, focus will be on key vocabulary,
concepts and problems covered on Exams 1 & 2 (Lectures 1-26) and
skills covered in Lab Exercises 1-8.
For example, everyone should know:
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differences between eukaryotic and prokaryotic cells
differences between replication, transcription, translation
how to read a genetic code table
how to fill in a simple dynamic programming matrix
differences between PAM and BLOSUM scoring matrices
how to retrieve sequences and structures from online databases
how to visualize and manipulate protein structures with PyMol
how to predict genes in a given DNA sequence
how to predict protein function from sequence
Strong hints:
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transcription/translation, dynamic programming & HMM
problems similar to those on Exams 1 & 2 are almost
guaranteed to appear!!
For the "New Material" part of Final Exam, focus will be on material
covered in:
ƒ Lectures 27 - 38 (not Lecture 39)
ƒ Lab Exercises 9 – 11 (not Lab 12)
ƒ Final Exam WILL include question(s) based on BCB
544 Project Presentations
Strong hints:
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You should understand basic principles of:
ƒ Phylogenetic analysis
ƒ Machine learning algorithms
ƒ Microarray and proteomics techniques & analysis
You should solve practice problems included in this Study
Guide: New Material (Part IB – New Material) - below
BCB 444/544 Fall 07
Study Guide Final – Dec 3
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Practice Problems for Part IA - Comprehensive Section (20 pts)
IA-1. Using this hidden Markov model and assuming that you start in state 1 calculate
the most probable path for sequence AGAT.
The most probable path is:
For complete credit, show your work by completing this probability table:
A
1
0.25
2
0
3
0
G
A
T
BCB 444/544 Fall 07
Study Guide Final – Dec 3
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Fill out the dynamic programming matrix for determining an optimal global
alignment between the sequences TCG and TCCAG. Scoring: +3 for matches; -2 for
IA-2
mismatches and spaces.
λ
T
C
C
A
G
λ
0
-2
-4
-6
-8
-10
T
-2
C
-4
G
-6
2.2 What is the score(s) of the optimal alignment(s) ? (Circle in the DP matrix)
2.3. There are 2 optimal alignments. For full credit, draw both of them below & show
your traceback arrows in the DP matrix above.
BCB 444/544 Fall 07
Study Guide Final – Dec 3
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Practice Problems & Review Questions for Part IB – New Material (40 pts)
IB-1. Phylogenetic Analysis
Find the parsimony score for the tree below using Fitch’s algorithm. Show your work.
C
A
G T
G
C
T
A
T
T
A
G
C
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Study Guide Final – Dec 3
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IB-2. Microarray Analysis – Clustering
Answer the following questions based on the provided table of correlation
coefficients for each pair of genes, calculated from microarray expression levels.
A
B
C
D
A
1.00
0.95
0.50
0.25
B
0.95
1
0.70
0.50
C
0.50
0.70
1
0.65
D
0.25
0.50
0.65
1
2.1 Using hierarchical clustering, how would you clusters genes (A,B,C,D)?
You may find it helpful to use the following table to calculate your clusters:
Iteration
1
2
3
Object 1
Object 2
Correlation
New Object
2.2 Draw a simple tree that illustrates this grouping of the genes.
In this Study Guide, a framework is provided – all you need to do is label the
leaves:
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Study Guide Final – Dec 3
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IB-3. Vocabulary & Short Answers Questions
What is/are:
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A perceptron?
A kernel function?
Parsimony?
Bootstrapping?
The Jukes-Cantor model?
A new high-throughput “massively parallel” sequencing technique?
The HAPMAP project?
SAGE?
The two main microarray platforms?
Two types of machine learning algorithms used to recognize patterns in
microarray data?
What are the main differences between:
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Brendel’s (ISU) GeneSeqer & Burge’s (MIT) GenScan programs for gene
prediction?
Supervised vs unsupervised machine learning algorithms?
Distance-based & parsimony-based phylogenetic tree-building algorithms
Regulation of gene expression in prokaryotes vs eukaryotes?
Hierarchical and k-means clustering?
Promoters & enhancers?
Cis- vs trans- acting regulatory factors?
Briefly list & describe the major sequence signals used in gene prediction software.
What are the two major types of distance-based methods for generating
phylogenetic trees – and what are the relative advantages and disadvantages
of each?
Why are SNPs important?
Which student project presentation did you find most interesting? Why? (Be
specific)
What is the most important “new” thing you learned in this course? Explain..
BCB 444/544 Fall 07
Study Guide Final – Dec 3
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Study Suggestions for Part II – Lab Practical (40 pts)
You will be given an amino acid sequence to a mystery protein. You will be
required to use servers/programs used in lab (such as BLAST) and to gather and
analyze information to characterize this mystery protein.
Knowledge of which servers perform which function will also be tested.
There will not be sufficient time to perform any analysis of actual microarray
data as part of the final practical. However, you should be prepared to discuss in
a paragraph or two some of the important issues in setting up a microarray
experiment, and how to normalize and filter your data prior to subsequent
analysis (e.g. clustering/machine learning etc.). This may be included as part of
the mystery protein portion of the practical, or as a standalone question or three.
For the practical, you will not be expected to discuss the clustering or
visualization portions of the lab, as there was less guidance about the best ways
to do this.
You will be expected to know how to retrieve structure files from PDB using
keyword search, direct retrieval by PDB id, or by BLAST query (either at PDB,
under Advanced Search, or using NCBI blastp, by specifying PDB as the database
to query). You will also be expected to use PyMOL to perform very basic
manipulations of how such a structure file is displayed.