COPE Course Unit

12.1 Course Objective

 

  1. To create awareness on bioinformatics concepts and practice and their application in Phytosanitary systems
  2. To sensitize participants on online resources available for bioinformatics
  3. To enhance knowledge and skills on interpretation and presentation of data

12.2 Course Outline

 

  1. Introduction to Bioinformatics & Online Resources
  2. Working with Single Sequences (Nucleotide)
  3. Sequence comparison & similarity searching
  4. Phylogenetics & Comparative Genomics

12.3 Course Content

 

1.1.1 Introduction to Bioinformatics & Online Resources (8hrs)
  1. Definition of bioinformatics
  2. Describe scientific context of bioinformatics and its application in Phytosanitary systems
  3. Describe the types of problems studied and solved with bioinformatics tools
  4. Explain the relationship between DNA, RNA and protein
  5. Introduction to BLAST
  6. Identify different types of databases and describe the information contained therein
  7. Retrieve relevant information from databases
1.1.2 Working with Single Sequences (Nucleotide) (8 hrs)
  1. Introduction to CLC main work bench and Bioedit
  2. Quality control of sequences
  3. Pairwise alignment and consensus
1.1.3 Sequence comparison & similarity searching (8hrs)
  1. Carry out BLAST on NCBI
  2. Interpret BLAST output
  3. Interpret expectation values
  4. Describe the importance of homology
  5. Introduction to BOLD and 16S databases
  6. Compare results from NCBI and BOLD data bases for DNA Barcoding sequences
1.1.4 Phylogenetics & Comparative Genomics (8hrs)
  1. Define phylogeny and explain how phylogenetic relationships can be established with bioinformatics
  2. Perform an alignment using ClustalW of a given FASTA sequence in MEGA
  3. Interpret multiple sequence alignments
  4. Estimate distances between sequences
  5. Construct phylogenetic trees from ClustalW results
  6. Describe tree construction algorithms
    1. UPGMA
    2. Neighbor-joining (NJ)
    3. Maximum likelihood (MJ)

vii. Construct trees using both NJ and MJ

vii. Use bootstrapping to evaluate tree quality

  1. Interpret phylogenetic tree results
1.2 Practical exercises (8 hrs)

Analysis of DNA barcoding sequences of fungi, bacteria, insect and plants

Analysis of virus sequences.

Construction of phylogenetic trees using different approaches

Exporting and saving the trees

References