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E-learning course on bioinformatics in animal viral pathogens

10 December 2014 - The use of sequencing for diagnosis and characterisation of pathogens has become very popular and is accessible by most veterinary laboratories that perform molecular testing. A nucleotide sequence contains information on the nature of the pathogen, its main features (type, pathogenicity, resistance to drugs, etc.) and its source. Bioinformatics provides tools to gather, store, and analyse these biological sequences, by dissecting and interpreting biological data from different organisms.

To support better prevention and control of animal diseases, the Food and Agriculture Organization of the United Nations (FAO) and the joint FAO/International Atomic Energy Agency (IAEA) division have provided several bioinformatics training courses to laboratory technicians, veterinarians and molecular epidemiologists from both diagnostic and research laboratories of FAO and IAEA Member States. They have also procured sequencing equipment and reagents and provided access to sequencing services to national veterinary laboratories. Furthermore they developed a collaboration with the Swiss Institute of Bioinformatics (SIB) for the development of an e-learning course on bioinformatics in animal viral pathogens.

The first module of this course, called "Phylogenetics of animal pathogens: basic principles and applications" was released to the public in 2013 (see related news). Designed as a self-learning module for animal health laboratory staff, it is organized in four chapters: 1) basic notions on phylogenetic trees; 2) how to build phylogenetic trees; 3) how to interpret phylogenetic trees, and 4) exercises. It includes many examples based on influenza, Foot-and-Mouth Disease and Peste des Petits Ruminants viruses. It requires about 4 hours to complete the entire course.

The second module, entitled “BLAST and multiple sequence alignment (MSA) programs” was released in May 2014. This module is subdivided into two parts that outline two of the main bioinformatics tools that help with the analysis of large amounts of sequences: the Basic Local Alignment Search Tool (BLAST) and the Multiple Sequence Alignment (MSA). This new module requires about 2 hours to complete the BLAST chapter and 2 hours for the MSA one.

BLAST is an algorithm that compares nucleotide or protein sequences to millions of known entries in sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. The self-learning chapter on BLAST includes: 1) basic notions on public databases; 2) notions on sequence similarity search; 3) a description of scoring systems; 4) a FastA/ BLAST sequence alignment programme; 5) a BLAST algorithm; and 6) how to interpret BLAST results.

MSA algorithms perform the most accurate alignment of three or more biological sequences and can be run on nucleotide or protein sequences. The output of MSA applications is used to study homology and the evolutionary relationship between the sequences studied. It also constitutes the basis to perform phylogenetic studies. Visual depictions of the alignment highlight mutation events such as point mutations (single amino acid or nucleotide changes), and insertion or deletion mutations (indels or gaps). The self-learning chapter on MSA includes: 1) description of the pairwise alignment scoring system; 2) difference between global versus local alignments; 3) notions on multiple alignment methods; 4) description of several MSA programmes; 5) how to edit alignments; and 6) software recommendations.

Several quizzes are available for the trainee to assess his/her understanding at each step of the modules.

All modules are accessible via a dedicated website and can also be distributed on CD-ROM and USB key.

FAO::: [email protected]
SIB ::: [email protected]


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Phylogenetics of animal pathogens: basic principles and applications

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BLAST and multiple sequence alignment (MSA) programs


  Comments: EMPRES-Animal Health webmaster

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