BMB511: Bioinformatica I (5 ECTS)

STADS: 01008301

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. Knowledge of Microsoft Windows is assumed.

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
None

Assessment and marking:

1. Approval of the exercise task sets, pass / fail, internal examiner at the teacher. Passing the exercise task sets is a prerequisite for the approval of the exercise report (b).
2. Approval of the exercise report. Pass / fail. Internal censorship.

Reexamination in the same exam period or immediately thereafter.

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

Forelæsninger (12 t.) og øvelser (30 t.).
(De angivne timetal er vejledende og der vil derfor kunne forekomme afvigelser.)
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.