Inhalt

[ 665GEDAGEDU11 ] VU Genomische Datenanalyse

Versionsauswahl
Es ist eine neuere Version 2016W dieser LV im Curriculum Bachelorstudium Molekulare Biowissenschaften 2016W vorhanden.
(*) Leider ist diese Information in Deutsch nicht verfügbar.
Workload Ausbildungslevel Studienfachbereich VerantwortlicheR Semesterstunden Anbietende Uni
6 ECTS B2 - Bachelor 2. Jahr Physik Irene Tiemann-Boege 4 SSt Johannes Kepler Universität Linz
Detailinformationen
Quellcurriculum Bachelorstudium Molekulare Biowissenschaften 2011W
Ziele Die Sequenzierung des Humangenoms wird heute als einer der wichtigsten Meilensteine in der Biologie betrachtet. Damit sind auch neue Disziplinen in der Biologie entstanden, die verschiedene genomische Fachrichtungen beinhalten. Der Kurs wird verschiedene Themen diskutieren, um den StudentInnen einen Einblick in die neuen Entwicklungen und technologischen Fortschritte in der Analyse von der genetischen Information zu geben. Als Praktikum werden die verschiedenen Datenbanken und deren Benutzung angesprochen werden, die heutzutage im jeden biologischem Feld die Forschung erleichtern.
Lehrinhalte (*)Part 1 -- Introduction to genomics

1. Introduction to genomics-3 case studies

  • Definition of bioinformatics/genomics
  • 3 study cases—why is genomics important?

- Finding a disease gene—Progeria story
- Synthetic biology—artificial genomes
- Evolutionary biology—What makes us human?

2. Genome projects / Comparative genomics

  • Sequencing Projects
  • Sequenced genomes
  • Understanding a genome sequence
  • Finding genes
  • Structural features

3. Genomic variation

  • Genomic variation
  • From SNPs to copy number variants and their evolution
  • HapMap project
  • Genotyping
  • Ethical issues
  • Human disease

4. The Human Genome Project

  • The Human Genome Project
  • Strategy of the human genome
  • Assembly
  • Main conclusions of the human genome project
  • Sequencing individual genomes

5. Emerging sequencing technologies

  • New sequencing technologies
  • Principles of new technologies
  • Commercial platforms
  • Sequencing RNA—replacement of expression arrays

Part 2 -- Introduction to databases (lab based)

1. Accessing information about DNA and proteins

* Genome browsers

  • Overview of the NCBI website
  • Accessing information: accession numbers and RefSeq
  • Entrez Gene (and UniGene, HomoloGene)
  • Protein Databases: UniProt, ExPASy
  • Three genome browsers: NCBI, UCSC, Ensembl
  • Access to biomedical literature

2. Sequence alignments

  • Pairwise sequence alignment
  • Definitions: homologs, paralogs, orthologs
  • Perform pairwise alignments (NCBI BLAST)
  • Assigning scores to aligned amino acids: Dayhoff’s PAM matrices
  • Alignment algorithms: Needleman-Wunsch, Smith-Waterman

3. How to use BLAST

  • BLAST-Basic local alignment search tool
  • How to use BLAST
  • How to interpret BLAST results
  • BLAST-like tools for genomic DNA

4. Advanced sequence search

  • PSI-BLAST
  • Multiple sequence alignment
  • Multiple ale alignment of genomic sequences

5. Finding a novel gene

  • Strategy to find a novel gene in the databases
Beurteilungskriterien (*)
  • Lecture: based on a series of quizzes, no computer, short answer / multiple choice.

Offered as a final exam or offered as small quizzes at the beginning of each

  • Laboratory: Results from computer lab—Report after each day
Lehrmethoden (*)The course will be taught in two parts. The first part will focus on the theoretical background of genomics including topics in genetics, molecular biology, and biochemistry. The second part will provide an introduction to the databases with step to step examples of how to retrieve different information. During the laboratory module students will work in groups to solve a series of problems based on the taught material.
Abhaltungssprache Englisch
Literatur (*)
  1. Bioinformatics and Functional Genomics by Jonathan Pevsner (Wiley-Blackwell, 2nd edition 2009).
  2. A Primer of Genome Science by Greg Gibson (Spencer V. Muse Publisher: Sinauer Associates, 3rd Edition 2008)
Lehrinhalte wechselnd? Nein
Präsenzlehrveranstaltung
Teilungsziffer 25
Zuteilungsverfahren Zuteilung nach Vorrangzahl