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Bioinformatic and Genomic School, UNESP, Sao Jose do Rio Preto, 28 May-8 June 2012

« Introduction to Bioinformatics applied to genomics »

 

Overview


The aim of this course is to introduce students in Biology to Bioinformatics. Bioinformatics is a science that uses computers to understand and store any biological information. Recent spectacular advances in nucleotide sequencing (so called NGS new generation sequencing technology) have revolutionized the research in biological sciences. These techniques that allow the sequencing of complete organisms in a couple of weeks, had led to the explosion of genomic sequences. These sequences have to be store and analyzed with automated procedures, that require competence in informatics and as well as the perfect knowledge in computational biology tools. Students will be trained in basic genomic concepts and tools to analyses large genomic sequences. Hand-on sessions (Practical course) will familiarized students with Linux OS, NCBI’s Entrez, Similarity searches, sequence alignments, EMBOSS, Galaxy and Artemis tools. Large sequencing data will be managed and analyzed by students. The basic principle of programming language will be also provided. 

The prerequisites are knowledge in molecular biology (e.g. structure of DNA/RNA, structure of genes) and skills in computer use.

 

Textbooks 

  • Bioinformatics for Dummies, Editor: Wiley Publishing; Authors: Jean-Michel Claverie, Cedric Notredame
  • Linux for dummies, Editor: Wiley Publishing; Authors: Dee-Ann LeBlanc
  • Developing Bioinformatics Computer Skills, Editor: O’Reilly; Authors: Cynthia Gibas and Per Jambeck.

 

Course materials 

A bootable USB key (8 Gi) with a Linux OS with pre-installed Bioinformatic tools will be delivered to each student.

 

Duration

10 Lectures and Practical courses on computer.

 

Course details  


 

  • Day 1: Introduction to Genome and Genomic analyses 

Lecture: Genomes, Sequencing and Annotation (databasegenome)

Practical: NCBI’s Entrez; Genome Browsers  (pdf)

Links: 

 

  • Day 2. Introduction to the Linux OS and Commands 
Lecture: Linux

Practical: Use of the Linux OS: A new world with a terminal. Basic commands, handle text files.

Links:

 

  • Day 3. Use of linux to the the first bioinformatic tools
Lecture:  Sequence cleaning and similarity searches and retrieving information.
Practical: BLAST searches and retrieve information.

Links:
 
  • Day 4. Software in bioinformatics: Use of BLAST and alignment tools
Lecture: Alignments tools 
Practical: Use of global and local alignment tools, introduction to phylogeny
 
Links:
 
  • Day 5. Handling sequences with EMBOSS

Lecture: Presentation of EMBOSS

Practical: Use of EMBOSS

Links:

 

  • Day 6. Transposable elements

Lecture: Transposable elements and plant biodiversity.

Practical: Annotation of Transposable elements 

Links :

 

  • Day 7. Annotation of BAC clones in Coffea  

Lecture: Annotation process

Practical: Annotation of a BAC clone in Coffea 

Links :  

 

  • Day 8. Expression data 
Lecture: Introduction to expression data. 

Practical: Manipulation and analysis of transcriptomic data. Example in Coffea pseudozanguebarie: Cleaning, assembly, Gene function and ontology.

Links:

 
  • Day 9. Comparative genomics/mapping sequences

Lecture: Mapping

Practical: mapping of sequences (genomic and transcriptomic) against genomic sequences.

Links: 

 

  • Day 10 (4 hours). Follow-up Lectures and Discussion. Exam.

  • Day Sup. Phylogeny
  • Links: Phylogeny.fr 
http://www.phylogeny.fr/

 

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