Genomics, Proteomics and Bioinformatics



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Genomics, Proteomics and Bioinformatics


Bio 224 — Fall 2010

Instructor: Dr. Tom Peavy


Office: SQU 406

Office hours: Tues/Wed 9:30-11 am (and by appointment)

Phone: 278-7276

Email: trpeavy@csus.edu

I. Class times


Lecture & Lab: Mon/Wed 2:00 - 4:15 PM

Location: Library room 128



II. Books

Textbook (TB): Bioinformatics and Functional Genomics

By Jonathan Pevsner (second edition; 2009)


Resource books:

Bioinformatics : Sequence and Genome Analysis (by David W. Mount; 2005)

Phylogenetics Made Easy. A How to Manual for Molecular Biologists

(by Barry Hall; 2001).


III. SacCT:

All resource materials for the course such as lecture PowerPts, assignments, web links, announcements, etc. will be uploaded to SacCT. A link to SacCT's logon site can be found on Sacramento State's homepage or using this web link https://online.csus.edu/webct/entryPageIns.dowebct. Lecture materials (PowerPt slides or pdf) can be accessed by 5pm the day prior to the lecture.


IV. Course Goals:

The overall goal of the course will be to apply and understand bioinformatics tools as they pertain to analyses of genomes, protein structure/function, gene families, and molecular evolution.


Learning Outcomes: Specifically you will be able to…

  1. Define what bioinformatics is and its importance in the sciences.

  2. Use bioinformatic software & tools to mine the databases to

explore questions about molecular structure, function and evolution.

  1. Illustrate how multiple alignments and data base searching are used to gather data about gene sequences.

  2. Perform advanced BLAST searches.

  3. Identify genes and infer gene structure.

  4. Differentiate between the types of phylogenetic analyses available and choose appropriate programs for specific questions.

  5. Design primers for PCR amplification.

  6. Decifer DNA sequencing chromatograms.

  7. Explain relationships between known protein structures and predicted protein structures.

10. Apply your bioinformatic knowledge to explore a gene family of your chosing.

V. Grading:
Participation 25 pts

Lab assignments 150 pts

Exam (1 @ 100 pts) 100 pts

Cumulative Project (written report) 150 pts

Cumulative Project Presentation 45 pts

Total semester points 470 pts


Final grades will be determined on a percentage basis according to the following scale:

93 -100 % A 73 – 76 % C

90 - 92 % A- 70 - 72 % C-

87 - 89 % B+ 67 - 69 % D+

83 - 86 % B 63 - 66 % D

80 - 82 % B- 60 – 62 % D-

77 – 79 % C+ < 60 % F
VI. Course Requirements for lecture and lab:

A. Class attendance and participation

B. Satisfactorily pass all the homework/laboratory assignments given.

C. Satisfactorily pass the exam

D. Satisfactorily meet all the criteria for the culminating project (oral and written).
A. Class attendance and participation:

There will be plenty of opportunities for class discussions and participation in class. Part of your success in this class will be based on how well prepared you are for class and your overall effort in the class. My policy for unexcused absences is as follows: one unexcused absence will be allowed; two absences will result in the loss of 10 pts; three absences will result in the loss of 20 participation points; four absences will result in the decrease of a full grade (e.g. AB) from their final grade (assessed without participation points); and five absences will result in an “WU” grade given for the course. Excused absences are medical emergencies (documentation required). In the case of absences, students will be responsible for gathering course information and turning in lab assignments by the due date.


B. Homework/Laboratory assignments:

You will have assignments to complete based on the lecture material. You will be given time to work on these assignments during class (in essence the laboratory portion of this class), but you will more than likely need to finish them on your own time. You must submit the assignments electronically (e-mail) to the instructor by midnight on the day stated as the deadline. Late assignments will be docked 2 ½ pts per day. If you miss class, it is important for you to download the weekly assignment found on SacCT and complete it prior to the deadline. Deadlines may be revised as deemed necessary and will be announced within SacCT and also in class.


C. Satisfactorily pass the exam.

One exam will be administered and will cover all the material from the prior class meetings (Nov 1). A review for the exam is scheduled during class time the week prior to the exam (Oct 25). The format will involve problem solving and critical thinking essay type questions. The exam is worth 100 points. A make-up exam will be given to a student only if the circumstances surrounding their absence was beyond their control, as determined by the instructor. In this case, I will require written documentation to verify the circumstance within one week of the missed exam.

D. Meet all the criteria for the culminating project (oral presentation and written report).

This will be an individual project where you will pick a gene of interest (that codes for a protein of reasonable size) and then apply your bioinformatic knowledge to understand it’s molecular structure, function and evolution. In other words, you will be applying the lessons learned directly from the homework assignments to this gene family (e.g. multiple sequence alignments, translations, phylogenetic analyses and protein modeling). This assignment will be turned in at the beginning of the last day of class on Wed, Dec 8th. Late projects will be docked 10 pts per day (includes weekend days). It is worth 150 points. Criteria for the written project will be provided later in the semester.


Students will present their cumulative project to the class during either the last day of class (Dec 8th) or during Finals week (Wed, Dec 15 at 12:45-3:30pm). Presentations should be approx. 10-15 minutes in length. You must be ready to present during your scheduled time slot or lose the points (45 pts). Criteria for the oral presentation will be provided later in the semester.
VII. Course policies

Cheating and plagiarism are not allowed. Cheating and plagiarism are very serious offences and will be prosecuted accordingly. The Department Chair and Dean of Students will be notified of the event and the student may be dismissed from the course with an “F”. Other possible lesser actions may be the loss of all points for the assignment/exam /report and/or reduction of the student’s final grade. Plagiarism is defined by the University as “the use of distinctive ideas or works belonging to another person without providing adequate acknowledgement of that person's contribution.” This includes website content!!! Students should review the University policy on plagiarism provided on the web (http://www.csus.edu/admbus/umanual/ump14150.htm).
VIII. Add/Drop Policy

The C.S.U.S. 2010-11 Class Schedule details the University’s add/drop policy. Students should evaluate whether they have the time to devote to the class before adding the class. In order to drop the course after the Census Date, students are required to provide documentation to verify their extenuating circumstances. Forms are available in the Biological Sciences Department office.


IX. Disabilities

Assistance will be provided to all individuals with a disability that affects their ability to succeed in the course. Students with disabilities should contact me as soon as possible (preferably in the first week) to arrange for reasonable accommodations.



TENATIVE LECTURE /LABORATORY SCHEDULE AND READING ASSIGNMENTS

Lecture Dates Topics Reading assignments

Aug 30 & Sept 1 Introduction & Review Genetics Chapter 1 & 2

Literature searches/ Sequence Data

[Assign #1 due Mon, Sept 13]
(Sept 6—Labor day; No class)
Sept 8, 13, 15 Pairwise Sequence Comparisons ` Chapter 3

and Scoring Matrices

[Assign #2 due Wed, Sept 22]


Sept 20, 22 BLAST Searches Chapter 4

[Assign #3 due Wed, Sept 29]


Sept 27 & 29 Protein Structure & Analyses Chapter 10

[Assign #4 due Wed, Oct 6]


Oct 4 & 6 Gene Expression Chapter 8

[Assign #5 due Wed, Oct 13]

Oct 11 & 13 Genomes and Gene Structure Chapter 16

[Assign #6 due Wed, Oct 20]

Oct 18 & 20 Multiple sequence alignments Chapter 6 [Assign #7 due Wed, Oct 27]
Oct 25, 27 Primer Analysis & DNA Sequencing Chapter 13

[Assign #8 due Wed, Nov 8]

Review for Midterm (Oct 25)
Nov 1 Exam
Nov 3, 8 & 10 Molecular Evolution & Phylogeny Chapter 7

[Assign #9 due Wed, Nov 17]



Project topic (due Nov 10)

Nov 15 & 17 Proteomics/Protein modeling Chapter 11

[Assign #10 due Wed, Nov 24]

Nov 22, 24, 29 PROJECT WORK DAYS

Dec 1, 6

Dec 8 Cumulative Project Due (beginning of class Wed Dec 8)



Approximately half of the students will present their cumulative projects
Dec 15 (Finals) The rest of the students will present their cumulative projects

(12:45-3:30 pm)


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