Course27633 >> Course program 2013
The Technical University of Denmark, Lyngby Campus, Building 306, Room 36 (room 38 from Jan 9). Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions.
The course runs every Thursday (Nov 14'th 2013 - Jan 17'th 2013 from 9:15 to 16 (or whenever the computer exercises of the day have been completed). Each day will start with lectures in the morning, and conclude with computer exercises in the afternoon starting normally at 13:00.
- Course materials:
The course materials include hand-out notes and the computer exercises themselves, which are relevant for the exam. Also, we will use supplementary information from the text book: Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0 which will be available in the DTU bookstore building 101.
Monday Jan 20'th 2014 a 4 hour written exam from 9-13 - bring your own computer and whatever notes you want to use. Exam in room 112+118 in building 210.
In case there is a need for a re-exam it will be Tuesday 25th Feb 2014 (but I hope this will not be an issue). A re-exam is for those of you that might get sick at the ordinary exam day or if you do not pass the course.
- Course description:
Required hardware / software
The computer exercises can be executed from any internet connected computer (Mac, Linux, Windows) with a modern browser (e.g. Firefox, Safari or Internet Explorer) and Java installed. Java is used in some exercises to run visualization software. Link: www.java.com
We recommend the JEdit text editor for use on sequence files, since it is free and well suited for this purpose and is platform independent. Link: www.jedit.org. You may also choose to use word that you provide yourself. In principle OpenOffice is ok, but we prefere that you use something else or at least save documents in word format.
For the protein structure exercise the PyMOL software (also cross-platform) will be used. Link: www.pymol.org.
Free Student's version: On Campusnet
If necessary, a username/password will be mailed to you, or provided at the course.
It is very important that you get custom/familiar with the reporting system as that is what we will use for the written exam in the end of the course.
After completing an exercise, upload it via Campusnet under the given day.
Make sure that the file that you upload has the correct format last name like .doc or .docx for word documents or .txt for simple text files and first name should be your student number and fi more files are uploaded then a period followed by any user text - examples could be:
The answers should be kept as minimalistic as possible - the important thing here is to focus on giving a nice and simple overview of your answers and not to spend a lot of time on fancy formatting. Minimalistic is good, but still avoiding to give too short answers like:
Answer: yes (rather 'yes' because of ...) Answer: 42 (rather explain how you got that number)
Write your name and study number in the top of every file For example:
Answers to the Multiple Alignment exercise ------------------------------------------ Report by: jens jensen (v18103)
As mentioned before jedit is a suitable text editor - download it here: jedit
Collection of links
- DNA and Amino acids
- Substitition matrices
- Alignment tools
- Prediction tools at CBS
Exam from previous years
Lecture Plan 2013 - 2014
Please note: lecturers may be working on slides and other course material until the last minute, so changes may occur!
Thursday November 14
- Lecture 1 - Introduction to the course - Thomas Nordahl Petersen
- Lecture 2 - Biological information, DNA structure and sequencing, GenBank searching - Henrik Nielsen.
- Lecture 3 - DNA, Amino Acids and Proteins - Thomas Nordahl Petersen.
- page 1-26 (top of p 26) in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
- Exercises - Henrik Nielsen. (Exercise helper: Bent Petersen.)
Thursday November 21
- Lecture 1 - Evolution and DNA - Anders Gorm Pedersen
- Lecture 2 - Amino acids & proteins part II - Thomas Nordahl Petersen
- page 41-47 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
- Exercises: Thomas Nordahl Petersen
- Learning amino acid properties by use of modeling kit - modeling by hand
Thursday November 28
- Lecture 1 - Substitution matrices and Log-odds scores - Thomas Nordahl Petersen
- Readings for lecture 1 and 2:
- Slides: ppt
- Lecture 2 - Global and local alignment - Thomas Nordahl Petersen
- Readings: for lecture 1 and 2
- Slides: ppt
Thursday December 5
- Other topics that we have heard about but need to followup?
- Lecture 2 - Introduction to Blast - Thomas Nordahl Petersen
- page 165-169 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
- Slides: ppt
- Exercises1: Thomas Nordahl Petersen
- INFO to exercise1 Make 3 random sequences, but only report numbers for 1 of the sequences. Omit question 4, In Question 5 use pre-calculated alignments. Question 8 is the last, the remaining questions are optional.
- Exercises2: Lav opgave 1,2 og 3 fra tidligere eksamenssæt jan2011 - pdf
Thursday December 12
- Exercise 1
- Extra material:
- Fun multiple alignment "game": Phylo
- Lecture 2 - Pylogenetic trees - Anders Gorm
- handout exercise Reconstruction of a distance tree
- Quiz 3 - uniprot, katalysisk aktive aminosyrer og Blast alignment
- Svar Quiz 3 pdf
Thursday December 19
- Lecture - Protein 3D-structure - Thomas Holberg Blicher
- page 95-100 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0. (Some background but Not exam material)
- page 109-111 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0. Relevant for exam.
- page 165-167 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
Thursday January 2
Thursday January 9
- Lecture 1 - Genome Browsers - Thomas Nordahl Petersen
Thursday January 16
- Lecture 1 - Entropy, Information Content & logo plots - Thomas Nordahl Petersen
- page 170-172 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
Monday January 20 exam
- Sluk telefonen og lad den ligge indtil efter eksamen
- Det er naturligvis ikke tilladt at kontakte andre via din computer - nettrafikken vil blive logget.
- God eksamen
Tuesday 25 February 2014 - re-exam (mundtlig)
Såfremt du/I ikke har bestået den skriftlige eksamen, er der mulighed for at gå op til en mundtlig eksamen. Man tilmelder sig ved at sende en mail til mig firstname.lastname@example.org med navn og studienummer senest d 18 Feb.