BMB511: Bioinformatica I (5 ECTS)

STADS: 01012601

Level
Bachelor course

Teaching period
The course is offered in the autumn semester.

Teacher responsible
Email: php@bmb.sdu.dk
Email: hjernoe@bmb.sdu.dk

Timetable
Show entire timetable
Show personal time table for this course.

Prerequisites:
None

Academic preconditions:
BMB506 Protein Chemistry alternatively BMB533 is presumed known.

The course cannon be taken by students that have passed BM131.

Course introduction
To give the student an insight in the use of Bioinformatics and the importance of biological databases in modern molecular biology. The student will through practical exercises with direct access to the most important biological databases obtain knowledge of bioinformatics and the associated biology.

Qualifications
The student will be able to have knowledge of the most important protein sequence databases, their structure and most important characteristics.
Make a homology search and evaluate the results.
Make a binary alignment of protein sequences and identify homology.
Make a multiple alignment.
Draw a phylogenetic tree based on homologous protein sequences.
Have a basic knowledge of 3D structure visualization.

Expected learning outcome
When the course is over, the students are expected to be able to:

• Search in article, protein and nucleotide databases and extract relevant information
• Recognize the general physical/chemical properties of DNA and RNA as well as properties which can help to predict genes within the pro- and eukaryotes.
• Search the protein motif databases and extract relevant information
• Perform homology searches in databases on the Internet and evaluate the results
• Make and evaluate binary and multiple alignments
• Build and evaluate phylogenetic trees
• Use prediction programs from the Internet for prediction of the physical and chemical properties of proteins, as well as evaluate the results
• Use simple programs to handle 3-dimensional protein structures
• Be familiar with the current resources and software available for bioinformatics on the Internet and critically evaluate whether the software works efficiently (ie, whether the analysis is correct and the results can be interpreted properly)
• Use the above methods for a comprehensive evaluation of sequences and structures

Subject overview

• Basic computer structure
• Sequence analysis
• Homology
• Function and identification
• Access to net based databases
• Searching in relevant databases on the World Wide Web
• Multiple sequence alignment
• phylogenetic trees

Literature

• Selzer, Paul Maria, Marhöfer, Richard, Rohwer, Andreas: Applied Bioinformatics, an introduction.
• Udleverede noter.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
Approval of the exercise task sets, pass / fail, internal examination by teacher.

Assessment and marking:
Written exam. Internal censorship, Danish 7-mark scale (5 ECTS).

Reexamination in the same exam period or immediately thereafter.

Date of exam
The ordinary exam takes place on January 27, 2016
The re-examination takes place on February 26, 2016

Expected working hours
The teaching method is based on three phase model.

Lectures (12 h) and exercises (30 hr).
(The specified number of hours is indicative and deviations are therefore likely to occur).
Educational activities

Language
This course is taught in English, if international students participate. Otherwise the course is taught in Danish.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.