Bioinformatic and Genomic school « Introduction to Bioinformatics applied to genomics », Sao Jose do Rio Preto (28 May-8 June 2012)








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. 








Organizers (Programa de Pós-Graduação em Genética)

Romain Guyot

Christine Tranchant-Dubreuil (UMR DIADE, IRD)

Claudia Carareto (University of Sao Paolo, Brazil)  




Course details


  • Day 1.Introduction to Genome and Genomic analyses

    Lecture: Genomes, Sequencing and Annotation

    Lecture: Use of Biological databases (NCBI)

    Practical: NCBI’s Entrez; Genome Browsers


  • 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.


  • 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.
  • 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

  • Day 5. Handling sequences with EMBOSS

    Lecture: Presentation of EMBOSS

    Practical: Use of EMBOSS

  • Day 6. Transposable elements
Lecture: Transposable elements and plant biodiversity.
Practical: Annotation of Transposable elements
  • Day 7. Annotation of BAC clones in Coffea
Lecture: Annotation process
Practical: Annotation of a BAC clone in Coffea
  • Day 8. Comparative genomics/mapping sequences
Lecture: Mapping
Practical: mapping of sequences (genomic and transcriptomic) against genomic sequences.
  • Day 9. Follow-up Lectures and Discussion. Exam.

  • Day Sup. Phylogeny
  • Day Sup. Galaxy

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