Genomic analysis and bioinformatics

- Knowledge and understanding of genomic analysis technologies and bioinformatics tools as well as their applications in different areas of society, in the field of biomedicine, in genetic breeding in agriculture and livestock, as well as in the conservation and management of genetic resources.

BLOCK 0: PRESENTATION OF THE SUBJECT (1 hour)
1. THEORETICAL CONTENT (36 hours)
Lecture classes (33 hours): Análise Xenóm e Bioinf.
BLOCK 1: GENOMIC ANALYSIS (14 horas)
Unit 1: Structural genomic analysis. Fragmentation of genomes. Chromosome isolation. Sequencing and assembly of genomes, from Sanger to NGS (Next Generation Sequencing) technologies.
Unit 2: Physical maps and genetic maps. Genetic markers. Genotyping by sequencing (GBS). High resolution maps and analysis of loci associated with quantitative traits (QTLs). Genomic association analysis (GWAS). Comparative genomics.
Unit 3: Functional genomics. Transcriptomics: Microarrays. RNAseq. Metagenomics. Proteomics. Regulomics.
BLOCK 2: BIOINFORMATICS (13 hours)
Unit 4: Bioinformatics and databases. Management and functional annotation of genomic and transcriptomic sequences. Gene prediction.
Unit 5: Sequence alignment and phylogenetic analysis. Genomic mining. Population and evolutionary genomics.

BLOCK 3: APPLICATIONS OF GENOMICS (6 horas)
Unit 6: Genomic analysis applied to Biomedicine. Precision medicine.
Unit 7: Applications of genomic analysis in agriculture and livestock. Analysis of productive and evolutionary interest traits. Marker-assisted selection. Genomic selection. Gene editing applied to production.
Unit 8: Application to the conservation and management of genetic resources. Characterization of conservation and management units. Genomic analysis of adaptive variability.

Seminars (3 hours)
Sem An. Xen. Bio. 1. Problems and questions concerning Block 1.
Sem An. Xen. Bio. 2. Problems and questions concerning Block 2.
Sem An. Xen. Bio. 3. Problems and questions concerning Block 2.

2. PRACTICAL CONTENTS (15 hours)
Laboratory practices (12 hours)
P A Xe Bio Lab F Vet 1 (3 hours). DNA sequencing using Sanger technology.
P A Xe Bio Lab F AI2 2 (3 hours). Obtaining data of interest in public databases. Management of multiple alignment of sequences (MAS).
P A Xe Bio Lab F AI2 3 (3 hours). Phylogenetic analyses of nucleotide sequences.
P A Xe Bio Lab F AI2 4 (3 hours). Introduction to the management of data obtained in new generation sequencing platforms.

Tutorial sessions in small groups (3 hours)
Tit. An. Xen. Bio. There will be activities in a small group (3-4) focused on each of the three blocks of theory.

BASIC BIBLIOGRAPHY
Brown T.A. 2023. Genomes. 5ª Edición. Taylor & Francis Group.
Brown T.A. 2008. Genomas. 3ª Edición. Editorial Médica Panamericana. Buenos Aires.
Gallego J. & Fernández A. 2019. Genómica y Proteómica. Editorial Síntesis. Madrid.
Lesk A.M. 2017. Introduction to genomics. 3ª Edición. Oxford University Press, Oxford.
Lesk A.M. 2019. Introduction to Bioinformatics. 5ª Edición. Oxford University Press, Oxford.
Pierce B.A. 2019. Genetics: a conceptual approach. 7th Ed. WH Freeman.

COMPLEMENTARY BIBLIOGRAPHY

Brown S.M. 2013. Next-Generation DNA Sequencing Informatics, 2nd Edition. CSH-Press.
Barnes M.R. 2007. Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data, 2nd Edition. Ed. Wiley-Blackwell.
Marco D. 2011. Metagenomics: Current Innovations and Future Trends. Ed. Caister Academic Press
Poptsova M.S. 2014.Genome Analysis: Current Procedures and Applications. Caister Academic Press

Knowledge:
Con7: To know and interpret the structure, organization, transmission, expression, regulation and evolution of genetic material.
Skills/abilities:
H/D05: To use appropriate techniques for the study of gene structure and function for the development of biotechnological applications.
H/D06: To analyze and evaluate the genetic, molecular and biochemical markers associated with the different pathologies critically.
H/D09: To interpret information from the main biological databases (genomic, transcriptomic, proteomic, metabolomic, etc.) and bibliographic data, using basic bioinformatics tools.
Competences
Comp01: To develop the ability to organize and plan work properly, based on a synthesis and analysis that allow decisions to be made.
Comp04: To act with professionalism for ethical principles, scientific rigor and sustainable development.

- Lectures classes (33 hours): the contents of the subject will be explained with the support of audio-visual presentations, with the help of annotations on the blackboard.
- Seminars (3 hours): The teacher will provide, via the virtual campus and with sufficient notice, bulletins with questions and unsolved problems related to the different topics of the program. The students will try to solve the bulletins before the sessions and autonomously in order to gauge their progress in the subject. In the seminars, the teacher will address the doubts raised by the students.
- Practices (12 hours): will experimentally deal, both with laboratory procedures and bioinformatics job, with genomic analysis methods that will complement the concepts developed in the theoretical classes. They will include an introduction and scripts detailing the procedures to be carried out under the supervision of the professor. At the end of the practices, students will discuss with the professor the results obtained in order to answer and deliver the questions posed in the script. Students will work in couples during laboratory sessions while they will individually work in informatics sessions..
- Tutorial sessions in small groups (3 hours): Group works will be carried out (3-4 students) focused on pioneer studies in the field of genomics, where students must extract the main methodologies used, the results obtained and the main conclusions. The face-to-face hours will be used for discussion between the different groups based on their studies, to reinforce the concepts developed in the theory classes.
- The USC Virtual Campus will be used continuously to support teaching.

It is recalled that, as stated in Article 16 of the Regulations for the Assessment of Students' Academic Performance and Review of Qualifications, approved by the Governing Council on 15 June 2011, "The fraudulent performance of any exercise or test required in the assessment of a subject will result in a failing grade in the corresponding exam session, regardless of the disciplinary process that may be followed against the offending student. Fraudulent work is considered to be, among others, plagiarised work or work obtained from publicly available sources without reworking or reinterpretation and without citation of the authors and sources".
The final score will be a weighted average of the qualifications obtained by the students in the different assessable teaching activities according to the following scale:
- Final exam: 70% of the final score (if the student passes the exam). Face-to-face exam on the date assigned by the Centre at the beginning of the Academic Year. It will consist of test type and/or questions that will require answers of greater or lesser length and the resolution of problems on the theory given in the lectures. Mandatory evaluable activity.
Competences evaluated: Con7, H/D05, H/D06, H/D09, Comp01
- Practices, 25% of the final score. Attendance, attitude and answers to the questions in the practical scripts will be scored. Non-mandatory assessable activity.
Competences evaluated: Con7, H/D05, H/D06, H/D09, Comp01, Comp04
- Tutorial sessions in small groups, the work carried out represents 5% of the final score. Aspects such as the quality of the extracted information, synthesis capacity and class participation will be assessed. Non-mandatory assessable activity.
Competences evaluated: Con7, H/D06, H/D09, Comp01, Comp04

EXPLANATORY NOTES:
SCALE: To pass the subject a minimum average score of 5.0 points (scale from 0 to 10) must be obtained in the theory exam. Once the exam has been approved (which represents 70% of the final score), the scores obtained in the remaining activities of the subject will be added with the scale described. In case of not reaching 5,0 points in the theory exam, the final score will be only the one obtained in the theory exam.
PRACTICES: Attendance is compulsory to pass the subject.
GROUP CHANGES: In practices, tutorials and seminars, group changes may be made whenever there is another student from another group with whom to change. These changes must be previously communicated by e-mail to the teacher responsible for the activity.
EXAM DATES: No exams will be held on alternative dates to the official ones.
SECOND OPPORTUNITY CALL: Students will have to do the exam, similar to that of the 1st opportunity call. The scores obtained in the remaining activities of the subject will be retained.
EXEMPTION FROM FACE-TO-FACE CLASSES ATTENDANCE: will be applicable to those students who have obtained it after applying for it according to the instruction nº 1/2017 of the General Secretary.

The subject consists of 6 ECTS credits. The total number of hours of student work is 150 hours, of which 36.6% are face-to-face and 63.4% are hours of autonomous student work (no face-to-face). The detailed distribution of student work time is as follows:
Student's work in classroom: 55 h
- Lectures classes: 33 h
- Seminars: 3 h
- Practices: 12 h
- Tutorial sessions in small groups: 3 h
- Exam and review: 4 h
Student's personal work: 95 h
- Individual study: 84 h
- Preparation of works: 11h

Attend all activities and ask questions that may arise during the development of these.
Continuous study based on the understanding of concepts.
Consult the recommended bibliography to enrich the contents treated during the development of the classes.
Use tutorials to resolve doubts or questions.

A virtual classroom will be operational on the Moodle platform available to students and direct communication channels through MS-teams.
RELEVANT INFORMATION: It is recalled that all the material that the teachers leave in the USC Virtual is subject to copyright, therefore its use outside this space will be considered fraudulent by not complying with the conditions of use of this classroom.