CS 609/BMI 609 Computational Genomics
Fall 2014
Credits: 3 units
Contact Hours: Monday and Wednesday 1400-1515
Instructors: Robert Edwards
Office: GMCS 536 Email: redwards@mail.sdsu.edu
Office Hours: Mondays and Wednesdays 1530 – 1700 (and by appointment)
Course Materials
1. CS 609 lecture notes/slides (available on Blackboard)
2. Supplementary textbooks:
i. Essential Bioinformatics by Jin Xiong ISBN: 0521600820
Course Information for CS 609
Description from the Official Course Catalog
Biological and genomics data. Application of computational algorithms to biological
questions. Post-genomic techniques in annotation and comparison of microbial and
eukaryotic genome sequences.
Prerequisites: Computer Science 503 or 514
Course Type: Selected elective course in the program
Specific Goals for CS 609
Course-Level Student Learning Outcomes
1. Ability to use existing bioinformatics algorithms to analyze genome sequences
2. Abtility to explain how those algorithms function and the complexity of the algorithm
3. Abtility to understand the merits of different bioinformatics algorithms
4. Ability to read, understand, and discussing relevant scientific literature
Relationship to CS Program Course Outcomes
CS 609 addresses the following CS Program course outcomes:
a) An ability to apply knowledge of computing and mathematics appropriate to the
program’s student outcomes and to the discipline
b) An ability to analyze a problem, and identify and define the computing requirements
appropriate to its solution
c) An ability to communicate effectively with a range of audiences
d) Recognition of the need for and an ability to engage in continuing professional
development
e) An ability to use current techniques, skills, and tools necessary for computing practice.
Topics Covered
The following topics are covered in CS 609:
1. Annotation
2. BLAST
3. Codon usage
4. Comparative genomics tools
5. DNA Sequencing
6. Hidden markov models
7. Machine learning
8. Metagenomics tools
9. Multiple sequence alignments
10. Pangenome analysis
11. Phylogeneomics
12. Protein families
13. Protein-encoding gene identification
14. Sequence alignments
15. Sequence assembly
16. tRNA identification
17. Whole genome comparisons
Course Schedule
Week
Topic
1
Introduction; DNA Sequencing, Sanger, Solexa, SOLiD, Ion
2
Sequence assembly; codon usage
3
Protein-encoding gene identification
4
tRNA identification; Multiple sequence alignments
5
Sequence alignments
October 6th 2014. The first progress report towards the final write up is due.
6
BLAST and International databases
7
Protein families
8
Hidden markov models
9
Whole genome comparisons
10
Annotation
November 10th 2014. The second progress report towards the final write up is due.
11
Comparative genomics tools
12
Pangenome analysis
13
Machine learning
14
Phylogeneomics - whole genome phylogeny
15
Metagenomics tools
December 10th, Final Report is due
Major assignments
Paper presentations
Everyone must present a paper in class, and we will have ~ 2 papers per week. Please choose
from the topics below and we will discuss the selections in class:
 General papers
 Annotation
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BLAST
DNA Sequencing
EST
HMMs
International Databases
Machine learning
Metagenomics
Protein encoding gene identification - ORF Calling
PanGenome Analysis
Protein families
RNA Identification
Sequence Alignments
Sequence Assembly
Structural Analysis
Whole Genome Comparisons
Whole Genome Phylogeny
Written assignments
The written assignment will be in three parts. At the beginning of the semester you will be
provided with a new genome to annotate. This is new sequence that has never been published
before. During the course of the semester you will identify the genes and proteins in that
genome, curate the annotations in that genome, and investigate the roles that the genome can
fulfill in the environment. The paper writing will accompany the dicussions in class.
At the end of the assignment you will have a complete article written in the format of Genome
Papers (http://genomepapers.org/) and ready for submission.
The first installment of the paper (due October 6th) will include basic statistics about the
organism and the genome that was sequenced The second installment (due November 10th) will
include information about the genes and functions that were found in the organism, and the third
installment due at the end of the semester will include a detailed description of the genome.
Grading Policies
The final grade will be comprised of:
In class participation: 35%
The written assingments will total 65% of the grade.
A
92 and above
A-
90-92
B+
88-90
B
82-88
B-
80-82
C+
78-80
C
72-78
C-
70-72
D+
68-70
D
62-68
D-
60-62
Fail
Below 60
Special Assistance
If you are a student with a disability and believe you will need accommodations for this class, it
is your responsibility to contact Student Disability Services at (619) 594-6473. To avoid any
delay in the receipt of your accommodations, you should contact Student Disability Services as
soon as possible. Please note that accommodations are not retroactive, and that accommodations
based upon disability cannot be provided until you have presented your instructor with an
accommodation letter from Student Disability Services. Your cooperation is appreciated.