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Analysis of Biological Sequences

Code:

BINF019

Sigla:

ASB

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia
OFICIAL	Informática

Ocorrência: 2022/2023 - 2S

Ativa?	Yes
Página Web:	https://stuntspt.gitlab.io/asb2023/
Unidade Responsável:	Departamento de Engenharia Química e Biológica
Curso/CE Responsável:	Undergraduate in Bioinformatics

Ciclos de Estudo/Cursos

Sigla	Nº de Estudantes	Plano de Estudos	Anos Curriculares	Créditos UCN	Créditos ECTS	Horas de Contacto	Horas Totais
BINF	21	Study Plan	2	-	5,5	67,5	148,5

Língua de trabalho

Portuguese - Suitable for English-speaking students
Obs.: Todos os slides estão em inglês

Objetivos

The purpose of this course is to introduce the basic principles biological sequences analysis, based on the concept of sequence (DNA, RNA and proteins), associated with the structure of biomolecules, to promotethe understanding of the applications of the various algorithms and to give the skills required to choose the most appropriate techniques and interpret the results obtained. The most common methods will bediscussed, as students should be able to understand and transcribe them into code, and the various tools available for analysis and treatment sequences will be studied in detail, so that students master them properly.

Resultados de aprendizagem e competências

Students will be able to recognize some of the common questions in the field of biological sequences analyses, and which methodologies are adequate to each such issue.
They will further be able to interpert and compare obtained results.

Modo de trabalho

Presencial

Programa

1. Biological sequences – DNA, RNA and proteins. Sequence contribution to biomolecule secondary and tertiary structure.
2. Pairwise sequence alignment – dot matrix and dynamic programming; gap alignment.
3. Multiple sequence alignment – dynamic programming, progressive methods and consensus sequence. Markov chains, introduction and application. ClustalW.
4. Searching for structural motifs – entropy, position matrices and Gibbs sampling.
5. Sequence alignment and searching in databases.
   5.1. BLAST algorithm and applications.
   5.2. Phyogenetics, phylogenetic trees and cladograms.
6. Bioinformatics software and interaction with databases
7. Applications – gene prediction, genetic expression data analysis and structure prediction

Bibliografia Obrigatória

Baxevanis, A.D., Ouellette, B.F.F.; Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Wiley Intersciente. ISBN: 978-0-471-38391-8
Borodovsky, M., Ekisheva, S.; Problems and Solutions in Biological Sequence Analysis, Cambridge University Press. ISBN: 978-0-521-61230-2
Mount, D.; ioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory Press. ISBN: 978-0-879-69712-9
Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G.; Biological Sequence Analysis: Probabilistic Models ofProteins and Nucleic Acids, Cambridge University Press. ISBN: 978-0-521-62971-3
Akihito, Akishinonomiya, F., Ikeda, Y., Aizawa, M., Nakagawa, S., Umehara, Y., Yonezawa, T., Mano, S., Hasegawa, M., Nakabo, T., & Gojobori, T.; Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses, Gene, 2016. ISBN: https://doi.org/10.1016/j.gene.2015.10.014

Métodos de ensino e atividades de aprendizagem

4 h/week of lectures and exercise classes in which the various topics will be exposed, intercalated with exercises on algorithms and exercises about study cases for application of the various bioinformatics tools.
Evaluation 1. Continuous: throughout the semester, various case studies will be proposed, which will be graded. Automated mechanisms will be put in place to mitigate academic fraud. Consequences of fraud will be consdered case-by-case, within the institution's regulation.

Software

Oracle VirtualBox

Tipo de avaliação

Distributed evaluation with final exam

Componentes de Avaliação

Designation	Peso (%)
Participação presencial	20,00
Apresentação/discussão de um trabalho científico	10,00
Trabalho escrito	70,00
Total:	100,00

Componentes de Ocupação

Designation	Tempo (Horas)
Apresentação/discussão de um trabalho científico	3,00
Estudo autónomo	32,00
Trabalho escrito	40,00
Frequência das aulas	60,00
Total:	135,00

Obtenção de frequência

Completion of 2 written assignments, and class participation/performance of homework.

Fórmula de cálculo da classificação final

Through continuous evaluation: Grade of "Scientific debate" * 0.1 + grade of "presential" elements * 0.2 + grade of "assignment 01" * 0.35 + grade of "assignment 02" * 0.35.

Through final exam: 100% exam

Melhoria de classificação

Written exam.