Course Information

Bi9060 Bioinformatics II – proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Ing. RNDr. Martin Marek, Ph.D., MBA (lecturer)
prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Jan Dvorský (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

Timetable

Mon 17. 9. to Fri 14. 12. Tue 11:00–12:50 B11/306

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Timetable

Mon 18. 9. to Fri 15. 12. Tue 11:00–12:50 B11/306

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Timetable

Mon 19. 9. to Sun 18. 12. Tue 11:00–12:50 B11/306

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Timetable

Tue 11:00–12:50 B11/306

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Timetable

Tue 11:00–12:50 B11/306

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW ( Bi5000 Bioinformatics I ) && ! 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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II - proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Timetable

Mon 16. 9. to Fri 6. 12. Tue 14:00–15:50 B11/306

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW ( Bi5000 Bioinformatics I ) && ! 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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II - proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Timetable

Tue 15:00–16:50 B11/306

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW ( Bi5000 Bioinformatics I ) && ! 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. 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.

Syllabus

• 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 Worl 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 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

Literature

• Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Teaching methods

lectures and class discussions

Assessment methods

Written test: 50 questions Oral examination: practical

Language of instruction

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II - proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.

Timetable

Thu 8:00–9:50 B11/306

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW ( Bi5000 Bioinformatics I ) && ! 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 9 fields of study the course is directly associated with, display

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.

Syllabus

• 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 Worl 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 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

Literature

• Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Teaching methods

lectures and class discussions

Assessment methods

Written test: 50 questions Oral examination: practical

Language of instruction

English

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II - proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.

Timetable

Thu 8:00–8:50 B11/306

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW ( Bi5000 Bioinformatics I ) && ! 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

• Analytical Biochemistry (programme PřF, N-BCH)
• Mathematical Biology (programme PřF, B-BI)
• Mathematical Biology (programme PřF, N-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• General Biology (programme PřF, N-BI)

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.

Syllabus

• 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 Worl 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 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

Literature

• Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Teaching methods

lectures and class discussions

Assessment methods

Written test: 50 questions Oral examination: practical

Language of instruction

English

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics

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)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science

Prerequisites

NOW ( Bi9061 Bioinformatics - practice ) && ! C9080 Bioinformatics
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.
The capacity limit for the course is 32 student(s).
Current registration and enrolment status: enrolled: 0/32, only registered: 0/32, only registered with preference (fields directly associated with the programme): 0/32

fields of study / plans the course is directly associated with

there are 7 fields of study the course is directly associated with, display

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.

Syllabus

• 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 Worl 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 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

Literature

• Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Teaching methods

lectures and class discussions

Assessment methods

Written test: 50 questions Oral examination: practical (in Czech or in English)

Language of instruction

English

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
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://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics

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)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
National Centre for Biomolecular Research – Faculty of Science

Timetable

Fri 8:00–9:50 F01B1/709

Prerequisites

NOW ( Bi9061 Bioinformatics ) && ! C9080 Bioinformatics
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.
The capacity limit for the course is 32 student(s).
Current registration and enrolment status: enrolled: 0/32, only registered: 0/32, only registered with preference (fields directly associated with the programme): 0/32

fields of study / plans the course is directly associated with

there are 7 fields of study the course is directly associated with, display

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.

Syllabus

• 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 Worl 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 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

Literature

• Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Assessment methods

Written test: 50 questions Oral examination: practical (in Czech or in English)

Language of instruction

English

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

Study Materials
The course can also be completed outside the examination period.
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

The course is not taught in Autumn 2024

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && ( NOW ( Bi5000 Bioinformatics ) || 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.

Learning outcomes

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

The course is not taught in Autumn 2023

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && ( NOW ( Bi5000 Bioinformatics ) || 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.

Learning outcomes

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

The course is not taught in Autumn 2022

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && ( NOW ( Bi5000 Bioinformatics ) || 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.

Learning outcomes

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

The course is not taught in autumn 2021

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && ( NOW ( Bi5000 Bioinformatics ) || 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.

Learning outcomes

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

The course is not taught in Autumn 2020

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && ( NOW ( Bi5000 Bioinformatics ) || 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.

Learning outcomes

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II – proteins

The course is not taught in Autumn 2019

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (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

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && ( NOW ( Bi5000 Bioinformatics ) || 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.

Learning outcomes

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.

Syllabus

• 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

Literature

• 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

Czech

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II - proteins

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)
prof. RNDr. Roman Pantůček, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW ( Bi5000 Bioinformatics I ) && ! 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

• Analytical Biochemistry (programme PřF, N-BCH)
• Mathematical Biology (programme PřF, B-BI)
• Mathematical Biology (programme PřF, N-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• General Biology (programme PřF, N-BI)

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.

Syllabus

• 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 Worl 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 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

Literature

• Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Teaching methods

lectures and class discussions

Assessment methods

Written test: 50 questions Oral examination: practical

Language of instruction

English

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

Bi9060 Bioinformatics II - proteins

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.

Prerequisites (in Czech)

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW ( Bi5000 Bioinformatics I ) && ! 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

• Analytical Biochemistry (programme PřF, N-BCH)
• Mathematical Biology (programme PřF, B-BI)
• Mathematical Biology (programme PřF, N-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• General Biology (programme PřF, N-BI)

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.

Syllabus

• 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 Worl 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 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

Literature

• Introduction to Bioinformatics, T.K. Attwood & D.J. Parry-Smith, Longman, Essex, 1999.

Teaching methods

lectures and class discussions

Assessment methods

Written test: 50 questions Oral examination: practical

Language of instruction

English

Follow-Up Courses

• B5000 PC Applications in Molecular Biology and Genetics
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every other week.

Teacher's information

http://loschmidt.chemi.muni.cz/peg/loadframe.html?courses.html

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