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Syllabus for

Academic year
UMF016 - Sequence information
 
Owner: BIMAS
4,0 Credits (ECTS 6)
Grading: TH - Five, Four, Three, Not passed
Level: C
Department: 0345 - MEDICINSK OCH FYSIOLOGISK KEMI GU


Teaching language: English

Course module   Credit distribution   Examination dates
Sp1 Sp2 Sp3 Sp4 No Sp
0101 Examination 4,0 c Grading: TH   4,0 c   16 Dec 2004 pm V

In programs

TKBIA BIOENGINEERING, Year 4 (elective)
TITEA INFORMATION ENGINEERING, Year 4 (elective)
BIMAS MSc PROGRAMME IN BIOINFORMATICS, Year 1 (compulsory)

Examiner:

Professor  Tore Samuelsson



Eligibility:

For single subject courses within Chalmers programmes the same eligibility requirements apply, as to the programme(s) that the course is part of.

Course specific prerequisites

UMF010 Introduction to Bioinformatics or equivalent.

Aim

Genetic information is stored in the DNA molecule as a linear sequence of bases. In the course of gene expression this sequence is translated into a sequence of amino acids in proteins. The sequence of amino acids in proteins in turn determines the three-dimensional shape and biological function of the protein. Analysis of DNA and protein sequences therefore plays an essential role in bioinformatics. Such analysis is aimed at for instance structural and functional prediction, classification of protein molecules, elucidation of the molecular basis for human genetic disease, or reconstruction of evolutionary history. The course presents the most important theoretical principles, as well as the applications and tools available in sequence analysis.

Content

Molecular biology databases and retrieval of data. Pairwise alignment. Heuristic searches. FASTA and BLAST algorithms. Multiple sequence alignment. Pattern matching. Pattern databases. Profiles. Psi-blast. Predicting sites and function in biopolymers. Promoters and transcription signals, RNA processing, splice site prediction, and prediction of coding regions. Neural network methods. Protein families: Prosite, Pfam. Whole genome analysis. What we can learn from the complete sequence of a genome. Comparative genomics. Analysis of a given pathway across genomes. Evolution and horizontal gene transfer. The effort to sequence the human genome. Human genetic disease and cancer.

Literature

Bioinformatics. Sequence and Genome Analysis.
David W Mount.
Cold Spring Harbor Laboratory Press, 2001.

Examination

Computer exercises, project, and written exam.


Page manager Published: Thu 03 Nov 2022.