Genetics 711/811 | Bioinformatics and Genomics

  1. Course Description:

    The methods, applications, and implications of genomics–the analysis of whole genomes. Microbial, plant and animal genomics are addressed, as well as medical, ethical and legal implications. The lab provides exposure and experience on a range of bioinformatics approaches–the computer applications used in genome analysis.

  2. Contact Information for Professor Matthew MacManes

  3. Lecture: MWF 11:10-12:00PM Rudman G89

  4. Lab: Friday 3:10-5:00PM Hewitt 301

  5. Web Resources:

  6. Assignments and Exams

    Weekly Assignments: These are assigned in lab, and typically involve some sort of sequence analysis and short answer questions. There will be 5 throughout the semester worth 20 points each (100pts total). You may work in groups, but you must submit your own report. These will be due 1 week after they are assigned, typically on Tuesday, unless otherwise instructed. NO late assignments accepted

    Exams: There will be 2 exams covering both lecture and lab material. Each will be worth 150 points. The dates for these will be October 9 and November 20. Makeup exams will be permitted only under extreme documented circumstances, or by prior approval (> 1 week) from Prof. MacManes.

    Final Project: The final project will consist of an oral presentation and written report of a topic related to genomics and bioinformatics. Projects must incorporate an implementation of the computational techniques we’ve learned about. The final project will be worth 200 points (150 written/50 oral). Oral presentations will occur during the last 2 days of class. Written reports will be due on the last day of class. You may work in groups (< 5 members - mix of grad and undergrad), with the understanding that expectations increase with group size, given division of labor. More details will be provided later in the semester.

    Participation: Attendance to the lab portion of the class is critical. We have 13 lab sessions. 10 points each, maximum of 120 points may be earned. One lab may be missed without penalty. Additional missed labs may be made up with prior approval (> 1 week) from Prof. MacManes

  7. Materials Needed

    Required Textbook: PRACTICAL COMPUTING FOR BIOLOGISTS (PCFB) 1st edition by Haddock and Dunn. It is available on Amazon new, used and for rent. I think that there is a Kindle version if that is your thing! It should also be available in the campus bookstore, but you may pay more there!

    Amazon Web services: For lab exercises, we will use the Amazon Computer Cloud (EC2). You will need to set up an account during the first lab, and will be given $100 to pay for the analyses you will run this semester. The EC2 interface will work properly in OSX and Linux operating systems. For those of you with Windows computers, you will need to install a terminal emulator (MobaXterm is one option), or use the OSX computers in the computer lab.

  8. Grades

    The grade scale is: 93-100=A; 90-92.99=A-; 87-89.99=B+; 83-86.99=B; 80-82.99=B-; 77-79.99=C+; 73-76.99=C; 70-72.99=C-; 67-69.99=D+; 63-66.99=D; 60-62.99=D-; Below 60=F

    Item Maximum Points
    Exams 300
    Final Project 200
    Homework 100
    Participation 120

    Total Points 720

  9. Course Policies

    Student conduct: Honesty is a core value at the University of New Hampshire. The members of this academic community require and expect one another to conduct themselves with integrity. The Student Rights, Rules and Responsibilities handbook (www.unh.edu/student/rights) explains UNH’s expectation for academic honesty and defines those actions that constitute academic misconduct with regard to exams, homework, plagiarism, computers, etc. The penalty for the first incident of cheating, plagiarism or other breaches of the university’s academic honesty policies will be an automatic F grade for that assignment. A second infraction will result in an F grade for the class. The Dean’s office will be notified and dismissal from the university could result.

    Disability Services for Students: The University of New Hampshire is committed to providing students with documented disabilities equal access to all university programs and facilities. If you have a disability requiring accommodation, you must register with Disability Services for Students (DSS). Contact DSS at 862-2607. If you have received an Accommodation Letter for this course from DSS, please meet with Prof. MacManes privately to review those accommodations.

  10. How to get an A. Receiving an A in this shall should be really easy (I mean it!), assuming you follow these basic guidelines.

    • Come to class and lab, pay attention, be interactive: Active learning far outcompetes passive, so while coming to class itself is good, interacting/asking questions will be much better.
    • Ask questions when your confused. Come to office hours, or schedule a time to meet.
    • Don’t cram! Study a little, several times per week. You will remember more, and the exams will be less stressful.
    • Read the book and use (with caution) online resources.

  11. Course Schedule - Subject to Change

    Week Reading Topic Lab
    31Aug   Intro to Bioinformatics and Molecular Evolution BLAST
    07Sept (No Class Mon)   Finding Data & Pairwise Alignment UNIX
    14Sept   BLAST Alignment
    21Sept   Advanced Search (BLAT/HMM/others) HMMER/RepeatMasker
    28Sept   Multiple Sequence Alignment fastA/fastQ processing
    05Oct   Sequence Read Analysis Transcriptome Analyses1
    EXAM OCT 09
    12Oct (No Class Mon)   RNA and Transcriptomics Transcriptome Analyses2
    19Oct   Gene Expression Measuring Gene Expression
    26Oct   Genome Evolution Genome Assembly
    02Nov   Genome Assembly Genome Analyses
    09Nov (No Class Wed)   Genome Analyses Long Reads
    16Nov   Population Genomics Bacterial Genome Annot.
    EXAM NOV 20
    23Nov (no Class Wed/Fri)   Personal and Medical Genomics UNIX
    07Dec   Ethics & Final Project Presentations No Lab