Course27633autumn2013

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Course27633 >> Course program 2013

Contents

General information

Where:

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.

When:

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.


Exam:

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.

Re-exam.

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:

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

  • Prediction tools at CBS

prediction servers


Exam from previous years

2011

2012

2013

answer

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
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 eller på spørgsmål 3!
  2. Exercise: The protein database UniProt

Thursday November 21

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 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


Exercises




Thursday December 5

Lecture 1 - reading frames & ORFs (short) - Thomas Nordahl Petersen
Slides: ppt
Other topics that we have heard about but need to followup?
small quiz - DNA & reading frames: pdf docx
small quiz - svar pdf


Lecture 2 - Introduction to Blast - Thomas Nordahl Petersen
Readings:
Slides: ppt


Handouts:


Exercises1: Thomas Nordahl Petersen
  1. Using Blast for sequence searches
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

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


Quiz 3 - uniprot, katalysisk aktive aminosyrer og Blast alignment
  • pdf docx NB ! Question 1 - only necessary if you upload the answers to campusnet.
  • Svar Quiz 3 pdf

Thursday December 19

Lecture - Protein 3D-structure - Thomas Holberg Blicher
Readings
Slides:
Exercises: Thomas Holberg Blicher

Thursday January 2

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


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

Thursday January 9

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


Lecture 2 - From genotype to phenotype - Valborg Gudmundsdottir
Slides:
Exercises:

Thursday January 16

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


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

Monday January 20 exam

Exam
  • 4 hour written exam from 9:00-13:00 room 112+118, building 210
  • Bring computer and any books you want
  • Et link til eksamenssæt for 2014 i pdf og word bliver vist her fra kl 9:00
  • Eksamen 20 Jan 2014 docx pdf
  • I vil også få udleveret en papir-version, som ikke skal afleveres.
  • 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 tnp@cbs.dtu.dk med navn og studienummer senest d 18 Feb.
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