THREE-DIMENSIONAL MODELING

Course objectives

Bioinformatics is the discipline that deals with the analysis and attribution of biological significance to the large amount of biomolecular data available today and represents an essential tool in the field of basic biochemical, biological-molecular, biomedical and research activities. biotechnology. The Bioinformatics Laboratory course aims to introduce the biology student to the use of the most common computational tools nowadays used in bioinformatic sequence analyzes and structures of both proteins and nucleic acids and the acquisition of knowledge on their functioning . Students who pass the exam will have acquired: a) knowledge and ability to understand the nature of biomolecular data the logical basis of the most common bioinformatic data analysis programs ability to process simple bioinformatic analyzes of data in the application and research fields b) ability to apply knowledge and understanding in the rational and effective use of the most common bioinformatics tools in the identification of the instrument suitable for the solution of a specific biological problem know how to plan the transfer of theoretical results to experimental practice c) autonomy of judgment know how to identify the limits of application of bioinformatics tools know how to interpret and critically apply the results obtained d) communication skills know how to illustrate the logic used to identify the bioinformatics tool suitable for solving a biological problem know how to communicate and explain the meaning of the facts during an oral interview e) learning ability the basic knowledge to progress autonomously in learning the use and operation of more advanced bioinformatics tools

Channel 1
STEFANO PASCARELLA Lecturers' profile

Program - Frequency - Exams

Course program
Description of the main biological databases and interrogation methods (2 hours) - Comparison of two sequences with exact and heuristic algorithms; comparison of two genomes (2 hours) - Score matrices (1 hour) - Searches in databases for sequence similarity (3 hours) - Methods for calculating multiple sequence alignments (4 hours) - Construction of profiles and PSSM (2 hours) - Searches with profiles in databases; profile databases (2 hours) - Hidden Markov Models (HMM) and use for database searches, sequence alignment, protein structure prediction, gene prediction (2 hours) - Neural networks and automatic classification algorithms; application to the prediction of secondary structures, solvent accessibility, signal peptides, antigenic epitopes, protein-protein interaction zones (2 hours) - Use of molecular graphics programs (2 hours) - Modeling by homology (2 hours)
Prerequisites
The optional course takes place in the second semester of the third year. To follow successfully, the student must possess: - notions of biological chemistry (protein structure, enzyme concept, basics of metabolism) - notions of Molecular Biology (concept of gene, genome, structure of nucleic acids, regulation of gene expression) - basic notions of statistics and probability theory (probability, probability distribution, statistical tests) - basic knowledge of the use of computers and internet browsing.
Books
The teaching material is available on the elearning site in the form of video lessons and pdf files. During the course, servers available on the internet and free programs will be used. Optional text: Pascarella Paiardini, Bioinformatics, Zanichelli
Teaching mode
Attendance of teaching lessons is not mandatory. The course is structured in theoretical and practical lessons that are held in a computerized classroom. The classroom is covered by the Sapienza WiFi signal and therefore students can also use their laptop for the practical part of the lessons. The theoretical part is illustrated through PowerPoint presentations and video projection of surfing websites. The practical part is carried out at the same time as the theoretical part using the sites that provide the bioinformatics methods described on your computer or on the computers available in the classroom. The practical part is interactive and allows the discussion and analysis of the results of the practical exercise carried out together with the teacher. The elearning2.uniroma1.it site contains the material shown during the lesson and the practical exercises that can thus be repeated autonomously and independently by the student, even remotely. The actual procedures will be decided on the basis of the current anticovid regulations.
Frequency
Attendance is optional but strongly recommended
Exam mode
The exam aims to verify the level of skill acquired in selecting and using the tools illustrated during the course. The evaluation is expressed out of thirty (minimum grade 18/30, maximum grade 30/30 with honors). The exam is divided into a practical test and a short interview. The practical test consists in solving three problems through the use of bioinformatics programs while the interview focuses on the discussion of the paper and on general theoretical topics. The final vote takes into account the two tests.
Bibliography
Loman, N., Watson, M. So you want to be a computational biologist?. Nat Biotechnol 31, 996–998 (2013). https://doi.org/10.1038/nbt.2740
Lesson mode
Attendance of teaching lessons is not mandatory. The course is structured in theoretical and practical lessons that are held in a computerized classroom. The classroom is covered by the Sapienza WiFi signal and therefore students can also use their laptop for the practical part of the lessons. The theoretical part is illustrated through PowerPoint presentations and video projection of surfing websites. The practical part is carried out at the same time as the theoretical part using the sites that provide the bioinformatics methods described on your computer or on the computers available in the classroom. The practical part is interactive and allows the discussion and analysis of the results of the practical exercise carried out together with the teacher. The elearning2.uniroma1.it site contains the material shown during the lesson and the practical exercises that can thus be repeated autonomously and independently by the student, even remotely. The actual procedures will be decided on the basis of the current anticovid regulations.
STEFANO PASCARELLA Lecturers' profile

Program - Frequency - Exams

Course program
Description of the main biological databases and interrogation methods (2 hours) - Comparison of two sequences with exact and heuristic algorithms; comparison of two genomes (2 hours) - Score matrices (1 hour) - Searches in databases for sequence similarity (3 hours) - Methods for calculating multiple sequence alignments (4 hours) - Construction of profiles and PSSM (2 hours) - Searches with profiles in databases; profile databases (2 hours) - Hidden Markov Models (HMM) and use for database searches, sequence alignment, protein structure prediction, gene prediction (2 hours) - Neural networks and automatic classification algorithms; application to the prediction of secondary structures, solvent accessibility, signal peptides, antigenic epitopes, protein-protein interaction zones (2 hours) - Use of molecular graphics programs (2 hours) - Modeling by homology (2 hours)
Prerequisites
The optional course takes place in the second semester of the third year. To follow successfully, the student must possess: - notions of biological chemistry (protein structure, enzyme concept, basics of metabolism) - notions of Molecular Biology (concept of gene, genome, structure of nucleic acids, regulation of gene expression) - basic notions of statistics and probability theory (probability, probability distribution, statistical tests) - basic knowledge of the use of computers and internet browsing.
Books
The teaching material is available on the elearning site in the form of video lessons and pdf files. During the course, servers available on the internet and free programs will be used. Optional text: Pascarella Paiardini, Bioinformatics, Zanichelli
Teaching mode
Attendance of teaching lessons is not mandatory. The course is structured in theoretical and practical lessons that are held in a computerized classroom. The classroom is covered by the Sapienza WiFi signal and therefore students can also use their laptop for the practical part of the lessons. The theoretical part is illustrated through PowerPoint presentations and video projection of surfing websites. The practical part is carried out at the same time as the theoretical part using the sites that provide the bioinformatics methods described on your computer or on the computers available in the classroom. The practical part is interactive and allows the discussion and analysis of the results of the practical exercise carried out together with the teacher. The elearning2.uniroma1.it site contains the material shown during the lesson and the practical exercises that can thus be repeated autonomously and independently by the student, even remotely. The actual procedures will be decided on the basis of the current anticovid regulations.
Frequency
Attendance is optional but strongly recommended
Exam mode
The exam aims to verify the level of skill acquired in selecting and using the tools illustrated during the course. The evaluation is expressed out of thirty (minimum grade 18/30, maximum grade 30/30 with honors). The exam is divided into a practical test and a short interview. The practical test consists in solving three problems through the use of bioinformatics programs while the interview focuses on the discussion of the paper and on general theoretical topics. The final vote takes into account the two tests.
Bibliography
Loman, N., Watson, M. So you want to be a computational biologist?. Nat Biotechnol 31, 996–998 (2013). https://doi.org/10.1038/nbt.2740
Lesson mode
Attendance of teaching lessons is not mandatory. The course is structured in theoretical and practical lessons that are held in a computerized classroom. The classroom is covered by the Sapienza WiFi signal and therefore students can also use their laptop for the practical part of the lessons. The theoretical part is illustrated through PowerPoint presentations and video projection of surfing websites. The practical part is carried out at the same time as the theoretical part using the sites that provide the bioinformatics methods described on your computer or on the computers available in the classroom. The practical part is interactive and allows the discussion and analysis of the results of the practical exercise carried out together with the teacher. The elearning2.uniroma1.it site contains the material shown during the lesson and the practical exercises that can thus be repeated autonomously and independently by the student, even remotely. The actual procedures will be decided on the basis of the current anticovid regulations.
  • Academic year2025/2026
  • CourseBiology
  • CurriculumBiotecnologico cellulare
  • Year3rd year
  • Semester2nd semester
  • SSDBIO/10
  • CFU3