Integrated course: Scientific method and linguisticsModule Computer science
Academic Year 2022/2023 - Teacher: GIOVANNI MICALEExpected Learning Outcomes
Objective of the course is the acquisition of methods for the analysis of biological sequences and structures and the capability of searching in in biological databases (eg. Genes, sequences, functional domains). Starting from primary sequences of nucleic acids or proteins can hypothesize the function, evolutionary history and structure. The tools used to achieve these objectives are the public databases and the tools for the analysis and visualization of such kind of data.
- Knowledge and understanding: Students will gain knowledge on methods for the analysis of biological sequences and for searching in biological databases. In particular students will be able to search on database of sequences and domains. Also, public databases available on NCBI will be presented together with software for the and the analysis and visualization of biological data. Finally, students will acquire the basic tools for the analysis of the transcriptome.
- Applying knowledge and understanding: identify the appropriate tools to manipulate data and extract knowledge underlying; solve problems through the use of appropriate software in bioinformatics.
- Making judgments: Through guided exercises, the students will acquire the basic skills necessary to deal with the analysis of new biological sequences, hypothesizing the function, study the transcriptome.
- Communication skills: the student will acquire the necessary communication skills and expressive appropriateness in the use of technical language within the general framework of the analysis of biological data.
- Learning skills: The course aims, as the goal, to provide students with the necessary basic theoretical methods and practices in order to address and solve problems concerning the analysis of biological data.
Course Structure
Lectures and practical exercises.
Should teaching be carried out in mixed mode or remotely, it may be necessary to introduce changes concerning previous statements, in line with the program planned and outlined in the syllabus.
Required Prerequisites
Attendance of Lessons
Detailed Course Content
The course is organized into lectures that provide a theoretical basis coupled with exercises for learning the use of bioinformatics tools in the field of medicine.
PROGRAM
- Introduction
- Pairwise and Multiple alignment
- Biological Databases: General Databases (NCBI, EMBL), Specialized Databases (OMIM, CIVIC, Drugbank, KEGG Pathway)
- Tools for the analysis of the transcriptome: Microarray, Next Generation Sequencing, Analysis of the transcriptome: Biomarkers
Textbook Information
We recommend the use of the text "Fondamenti di bioinformatica", Authors: Manuela Helmer Citterich Fabrizio Ferrè Giulio Pavesi Graziano Pesole Chiara Romualdi, Zanichelli Publisher (2018).
Other updated resources will be indicated by the lecturer in the slides used in class.
Course Planning
| Subjects | Text References | |
|---|---|---|
| 1 | Introduction to bioinformatics: data types, problems, tools. | Zanichelli Chapters 2 and 16. |
| 2 | Biological evolution: orthologs and paralogs | Zanichelli Chapter 4. |
| 3 | Pairwise alignment: basic concepts, alignment theory, formats, BLAST algorithm | Zanichelli Chapter 5. |
| 4 | Multiple alignment: basic concepts, phylogenetic trees, CLUSTALW algorithm and neighbor-joining. | Zanichelli Chapter 6. |
| 5 | Hands-on activity on sequence alignment. | Materials provided by the lecturer. |
| 6 | General biological databases: NCBI (Gene, Nucleotide, Protein, SNP, Pubmed), Uniprot | Materials provided by the lecturer. |
| 7 | Biological databases for medicine: OMIM, Kegg Pathway, CIVIC, Drugbank. | Materials provided by the lecturer. |
| 8 | Hands-on activity on biological databases. | Materials provided by the lecturer. |
| 9 | The basis of transcriptome analysis. | Zanichelli Chapter 10. |
Learning Assessment
Learning Assessment Procedures
The final exam consists of a written test or an oral interview at the teacher's discretion.
The written test consists of exercises and theory questions for 1 hour. The written test could be conducted through acomputer on the exam.net platform.
Unless otherwise announced, the written exam is held at 9:00 a.m.
Notes:
- To take the exams, it is mandatory to make reservations using the appropriate form on the student portal.
- Late reservations via email are not allowed. If no reservation is made, the exam cannot be verbalized.
- The exam might also be conducted electronically, should conditions require it.