Course27633autumn2011

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Course27633 >> Course program 2011

Contents

General information

Where:

The Technical University of Denmark, Lyngby Campus, Building 208, Room 062 (in the basement) in 2011. Teaching in Janurary 2012 will be in other rooms - see info for the teaching on the individual days. Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions.

When:

The course runs every Thursday (Nov 10'th 2011 - Jan 26'th 2012 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.


Exam:

Thursday Jan 26'th a 4 hour written exam from 9-13 - bring your own computer and whatever notes you want to use. Exam in room 042+048 in building 210.

Re-exam.

In case there is a need for a re-exam it will be Feb 27 2012 (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:

kursus databasen


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.


Reporting

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.

Campusnet aflevering

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:

 s12345.doc
 s12345.1.doc
 s12345.2.doc
 s12345.homology.txt


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

DNA translation table

Amino acids

  • Databases

UniProt database

PDB protein DataBank

Genbank

  • Substitition matrices

Substitution matrices introduction

Blosum62 matrix

  • Alignment tools

Pairwise sequence alignment Embl-ebi

Blast via ncbi

Lecture Plan 2011 - 2012

Please note: lecturers may be working on slides and other course material until the last minute, so changes may occur!

Thursday November 10

Lecture 1 - Introduction to the course - Thomas Nordahl Petersen
Slides
Lecture 2 - Biological information, DNA structure and sequencing, GenBank searching - Henrik Nielsen.
Readings:
Slides:
Handouts:
Lecture 3 - DNA, Amino Acids and Proteins - Thomas Nordahl Petersen.
Readings:
Slides:


Exercises - Henrik Nielsen. (Exercise helper: Bent Petersen.)
  1. Exercise: Searching the GenBank database NB: I behøver ikke at svare på spørgsmål 1.3!
  2. Exercise: The protein database UniProt

Thursday November 17

Lecture 1 - Evolution and DNA - Anders Gorm Pedersen
Reading:
Slides:


Lecture 2 - Amino acids & proteins part II - Thomas Nordahl Petersen
Readings
Slides:
Exercises: Thomas Nordahl Petersen
Learning amino acid properties by use of modeling kit - modeling by hand



Thursday November 24

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
Exercises



Thursday December 1

Lecture 1 - Introduction to Blast - Thomas Nordahl Petersen
Readings:
Slides:
Handouts:


Lecture 2 - Psi-Blast - Iterative Blast searches and Position Specific Scoring Matrices - Bent Petersen
Readings:
Slides:
Exercises: Thomas Nordahl Petersen - Bent Petersen
  1. Using Blast for sequence searches
  2. svar

Thursday December 8

Lecture 1 - Multiple alignments - Anders Gorm
Slides
Readings:
Exercise 1
Extra material:
  • Fun multiple alignment "game": Phylo


Lecture 2 - Pylogenetic trees - Anders Gorm
Slides:
Readings
Handouts:
Exercise 2

Thursday December 15

Lecture 1 - Protein 3D-structure - Thomas Blicher
Readings
Lecture 2 Homology modeling - Thomas Blicher
Readings:


Slides:
Exercises: Thomas Blicher - Thomas Nordahl Petersen

Thursday January 5 Room 162 Building 210

Lecture 1 - Genome Browsers - Thomas Nordahl Petersen
Slides:
Readings:
Exercises:


Lecture 2 - From genotype to phenotype - Kasper Nielsen
Slides:
Exercises:

Thursday January 12 - room 162 building 210

Lecture 1 - Introduction to neural networks - Thomas Nordahl Petersen
Slides:


Exercise 1: Thomas Nordahl Petersen
Exercise 2: Thomas Nordahl Petersen

Thursday January 19 - room 018 building 210

Lecture 1 - Entropy, Information Content & logo plots - Thomas Nordahl Petersen
Readings:
Handouts:
Slides:


Lecture 2 - Summary - Thomas Nordahl Petersen
Slides:
Exercises: Thomas Nordahl Petersen

Thursday January 26, room 042+048, building 210

Exam
  • 4 hour written exam from 9-13
  • Building 210 - Room 042+048
  • Bring computer and any books you want
  • I recommend you bring a mouse, in case you need to work with PyMol, but your touchpad may work for you (no guarantee)
  • Link to exam word-document once exam has started
  • Link to exam pdf-document once exam has started
  • Link to exam word97-dokument once exam has started

Monday February 27 - re-eksamen (mundtlig), room 062, building 208

 Du skal møde op i rum 062 og trække et spørgsmål, herefter får du forberedelse som
 foregår i rum 027, hvor censor eller jeg lige følger dig på plads.


 Eksamen foregår ved at du trækker et spørgsmål, som indeholder en mindre
 praktisk opgave inden for pensum. Du vil så få 30 minutters
 forberedelsestid, hvor du skal løse den opgivne opgave ved hjælp af din
 computer. Du vil have adgang til DTU's trådløse internet. Lad alle
 relevante vinduer være åbne, så du bagefter kan vise, hvad du har gjort.
 Eksaminationen vil derefter vare ca. 20 minutter og tage udgangspunkt i
 din egen fremlæggelse af hvordan du har løst opgaven. Der kan dog også
 forekomme spørgsmål i andre dele af pensum. Karakteren vil blive givet
 umiddelbart efter din eksamen.


 I får en mail fra mig om hvilket tidspunkt I hver især skal møde op til.


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