C9080 Bioinformatics

Faculty of Science
Autumn 2003
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Chemistry Section – Faculty of Science
Prerequisites
ability to study in English
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The aim of this course is to give an introduction to Bioinformatics. Bioinformatics covers different computer applications in biological sciences and in its broadest sense the Bioinformatics means information technology applied to the management and analysis of biological data. The course will consist of theoretical part followed by practical training using computers and Internet. An introduction will be given to the theory of genome and protein information resources, to the DNA and protein sequence analysis, to the organization and searching of primary and secondary databases, etc. In its practical part, the course will demonstrate a number of the programs on the Internet that are used most commonly in DNA and proteomic research.
Syllabus
  • OPENING what is it Bioinformatics? study material organization lectures examination I. INTRODUCTION history of sequencing what is it Bioinformatics? sequence to structure deficit genome projects why is Bioinformatics important? patter recognition and prediction folding problem sequence analysis homo/analogy and ortho/paralogy II. INFORMATION NETWORKS what is the Internet? how do computers find each other? FTP and Telnet what is the Worl Wide Web? HTTP, HTML and URL EMBnet, EBI, NCBI SRS and ENTREZ III. PROTEIN INFORMATION RESOURCES biological databases - introduction primary protein sequence databases composite protein sequence databases secondary databases composite secondary databases protein structure databases protein structure classification databases IV. GENOME INFORMATION RESOURCES primary DNA sequence databases specialised DNA sequence databases V. DNA SEQUENCE ANALYSIS why to analyse DNA? gene structure gene sequence analysis expression profile, cDNA, EST EST sequences analysis VI. PAIRWISE SEQUENCE ALIGNMENT database searching alphabets and complexity algorithms and programs sequences and sub-sequences identity and similarity dotplot local and global similarity pairwise database searching VII. MULTIPLE SEQUENCE ALIGNMENT multiple sequence alignment consensus sequence manual methods simultaneous and progressive methods databases of multiple sequence alignments hybrid approach for database searching VIII. SECONDARY DATABASE SEARCHING why search secondary databases? secondary databases regular expressions fingerprints blocks profiles Hidden Markov Models IX. ANALYSIS PACKAGES commercial databases commercial software comprehensive packages packages for DNA analysis intranet packages Internet packages X. PROTEIN STRUCTURE MODELLING protein structure protein structure databases prediction of secondary structure prediction of protein fold prediction of tertiary structure modelling of protein-ligand complexes
Literature
  • Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.
Assessment methods (in Czech)
Written test: 100 questions (1 point / question), 100-90 points = 1, 89-80 points = 2, 79-60 points = 3 Oral examination: example sequence - search, analysis, modelling, prediction (in Czech or in English)
Language of instruction
English
Follow-Up Courses
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
Teacher's information
http://ncbr.chemi.muni.cz/~jiri/courses.html
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 2001, Autumn 2002, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008.
  • Enrolment Statistics (Autumn 2003, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2003/C9080