Bi9060 Bioinformatics II – proteins

Faculty of Science
Autumn 2018
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Ing. RNDr. Martin Marek, Ph.D. (lecturer)
doc. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Jan Štourač (seminar tutor)
Mgr. Martina Damborská (assistant)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology - Biology Section - Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.
Supplier department: Department of Experimental Biology - Biology Section - Faculty of Science
Mon 17. 9. to Fri 14. 12. Tue 11:00–12:50 A11/306
Prerequisites (in Czech)
( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && ( NOW ( Bi5000 Bioinformatics I ) || SOUHLAS ) && ! C9080 Bioinformatics
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
there are 6 fields of study the course is directly associated with, display
Course objectives
The aim of this course is to give an introduction to Bioinformatics. 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. The students will be able to understand the basic principles of bioinformatics and to use basic tools and databases for solving practical problems. They will be able to handle different types of data by analogy with examples learned during the course.
  • I. OPENING what is it Bioinformatics? study material organization lectures examination
  • II. 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
  • III. INFORMATION NETWORKS what is the Internet? how do computers find each other? FTP and Telnet what is the World Wide Web? HTTP, HTML and URL EMBnet, EBI, NCBI SRS and ENTREZ
  • IV. PROTEIN INFORMATION RESOURCES-I biological databases - introduction primary protein sequence databases composite protein sequence databases
  • V. PROTEIN INFORMATION RESOURCES-II secondary databases composite secondary databases protein structure databases protein structure classification databases
  • VI. GENOME INFORMATION RESOURCES primary DNA sequence databases specialised DNA sequence databases
  • VII. DNA SEQUENCE ANALYSIS why to analyse DNA? gene structure gene sequence analysis expression profile, cDNA, EST EST sequences analysis
  • VIII. 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
  • IX. MULTIPLE SEQUENCE ALIGNMENT multiple sequence alignment consensus sequence manual methods simultaneous and progressive methods databases of multiple sequence alignments hybrid approach for database searching
  • X. SECONDARY DATABASE SEARCHING why to search secondary databases? secondary databases regular expressions fingerprints blocks profiles Hidden Markov Models
  • XI. ANALYSIS PACKAGES commercial databases commercial software comprehensive packages packages for DNA analysis intranet packages Internet packages
  • XII. 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
  • XIII. BIOINFORMATICS IN PRACTICE-I Information networks Protein information resources Genome information resources DNA sequence analysis
  • XIV. BIOINFORMATICS IN PRACTICE-II Pairwise sequence alignment Multiple sequence alignment Secondary database searching Protein structure modelling
  • Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.
Teaching methods
lectures and class discussions
Assessment methods
Written test: 25 questions Minimum correct answers for passed: 17
Language of instruction
Follow-Up Courses
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
Teacher's information
The course is also listed under the following terms Autumn 2010 - only for the accreditation, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017.
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