Bioinformatics for Biochemistry Masters Program Dr Abdelkrim Rachedi
Bioinformatics for Biochemistry Master’s Program Dr. Abdelkrim Rachedi
Course program 1. General introduction to bioinformatics. 2. Databases in biology: -> 2. 1. Introduction to databases in general. -> 2. 2. Databases for the primary structure of Proteins and Nucleic Acids, access and usage. -> 2. 3. Sequence Alignment concepts, methods and applications. -> 2. 4. Databases for the structural data of Proteins and Nucleic Acids, access and usage. -> 2. 5. Structural Alignment concepts, methods and applications. 3. Algorithm in biology: -> 3. 1. Introduction to Algorithms in general. -> 3. 2. Sequence Alignment algorithms and weighing matrices. -> 3. 3. Structural Alignment algorithms and weighing matrices. -> 3. 4. 3 D-Structure prediction algorithms and applications.
Course program 4. Macromolecules 3 D-structure determination methods; strengths and weaknesses: -> 4. 1. Concepts of X-ray Crystallography Method. -> 4. 2 Concepts of Synchrotron X-Ray Diffraction Method. -> 4. 3. Concepts of Nuclear Magnetic Resonance Method. -> 4. 4. Concepts of Cryo-Electron Microscope Method. -> 4. 5. Concepts of SAXS Method. 5. Analyse de la structure 3 -Dimentionel des Macromolecules (protéines et acides nucléiques): -> 5. 1. Methods of macromolecular structure analysis. -> 5. 2. Evaluation of macromolecular structure. -> 5. 3. Impact of macromolecular structure quality on understanding the biological function.
Course program 6. Molecular modeling of 3 D-structure and function of proteins: -> 6. 1 Concepts. -> 6. 2 Algorithms. -> 6. 3 Methods. -> 6. 4 Applications. -> 6. 5 Reliability of the generated models and conclusions. 7. Ligands Binding and Drug Design: -> 7. 1 Introduction about Ligands and Drugs. -> 7. 2 Calculation of Ligands Binding Environment and Active Site. -> 7. 3 Macromolecular binding motifs and Ligands. -> 7. 4 Drug Design concepts and applications. -> 7. 5 Modeling new drugs and Technics of Molecular Docking.
DATABASES Introduction to databases
What is a database? A database is an organized collection of data. usually in a digital form. (for example a database for students information at an institute). The database is created to support processes requiring these information (for example, finding names and marks of successful students. . etc. ) ● A database typically is run via a database management system (DBMS). ● The database data collection with the DBMS is called a database system. ●
Progressive Example (example towards practical databases concept) Suppose you have a list of students’ information (names, telephones, e-mails, address, marks. . ) and need to store them. You could: ● Write them on a piece of paper. . (if few info. ) ● Store them in cell phone (mobile). . (if “many”) ● Use Excel. . (“reasonably” large data sets. . ) ● Use Access database. . (“reasonably” large data sets. . )
Progressive Example (example towards databases concept) …… Take notes about the progressive practical on Excel. …… ● Conclusions from the Excel practical: ● Redundancy problems with large and complex data. ● Complex data needs more than one table ● ● Data integrity & Efficiency for data management necessitate tables to be related “relational database” database Searching and presenting data in meaningful way need a some sort of querying language (like SQL. . see next)
SQL SQL: Structured Query Language, pronounced “sequal”, is a programming language aimed at managing in relational database management systems (RDBMS). ● Example SQL: select first_name, email_address, mark from students, emails, marks where mark>10 Example output: first_name email_address Mokhtari mkh@gmail. com Salem slm@yahoo. com marks 12 15
Microsoft Access (a database system) …… Take notes about the progressive practical on the Access databases. …… ● Access is part of the Microsoft Office. ● Access is PC based database ● Can be used to create tables with keys (relational aspect) ● Supports SQL for querying and output reports. . Etc.
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