South East Asian Training Course on

Bioinformatics Applied to Tropical



A workshop Sponsored by UNDP/World

Bank/WHO Special Programme for Research and

Training in Tropical Diseases (TDR)




International Centre for Genetic Engineering and

Biotechnology (ICGEB)


New Delhi, India

22nd September, 2003&endash; 6th October, 2003*



The Regional Training Course on Bioinformatics (Computational Biology) applied to Tropical Diseases Genomics is an initiative designed as a part of the activities of WHO/TDR in collaboration with International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India. The aim of this initiative is to promote capability of endemic countries scientists to apply cutting edge DNA technology to tropical diseases research. The objective is to introduce the participants to basic information on the application of genome information and the potential for development of tools that can be applied in tropical diseases research. The regional two-week training course will focus on bioinformatics (computational biology) concepts and applcations with specific emphasis on the tropical diseases in TDR portfolio (Malaria, Tuberculosis, Dengue, Leishmaniasis, Chagas' disease, African sleeping sickness, Leprosy, Filariasis, Onchocerciasis, and Schistosomiasis).

Seascape will feature Tripos products and services via a seminar presentation and a two day workshop from Oct 3-Oct 6th.

Course objectives and goals:

The objective of the course is to train young investigators and encourage application of bioinformatics/computational biology to pathogen genome research and development of new products against tropical diseases. Effort on the course will also be devoted to promoting multidisciplinary and international networking in order to facilitate South-South and North-South collaborations in computational biology/bioinformatics and tropical diseases research.

The training course will run for 2 weeks. Preference will be given to scientists with strong evidence and potential to apply the knowledge and expertise gained from the course to research and also to train others to increase bioinformatics capacity at their home institution. The course will consist of lectures and theoretical sessions in the morning (09:00-12:30), and hands-on practical training sessions in a computer laboratory in the afternoon (14:00-17:30) given by invited speakers and experts from India and international institutions. There will be evening sessions for follow-up and scripting exercises. A personal computer will be provided to each participant. Participants will receive training materials and documentation on main topics covered by the course, and will have access to the support services provided by the centre.

Course Website:

Course Content:

Overview of pathogen genomes and genomics.

  • Introduction to computing basics: hardware, operating systems, networks.
  • Installing Linux; file formats & conversion.
  • Installing software on local machines (downloading & decompressing BLAST, Phylip, ClustalW, etc).
  • Genome sequencing, sequencing technology and strategies.
  • Sequence retrieval, formats, sequence analysis, genome scaffold assembly, contig assembly and ordering, sequencing editing, computational approaches to facilitate gap closure.
  • Gene Prediction and identification.
  • Identifying functional motifs and structural domains by comparing sequences against PROSITE, BLOCKS, SMART, Pfam, CDD databases, Prodom, Trembl,Interpro.
  • BLAST &endash; pair-wise alignments and setting up local blast.
  • CLUSTALW - multiple alignments.
  • NCBI resources.
  • PERL
  • EMBL resources.
  • Role of Bioinformatics in vaccine and drug development.
  • Basics of GCG, EMBOSS and Staden.
  • Protein structure prediction: Introduction to protein structures and different generations of prediction software
  • Downloading PDB database files, displaying using molecular graphics &endash; Rasmol
  • Protein structure prediction: Different prediction strategies: Statistical methods, Homology, Threading, Chou Fasman methods, neural network and genetic algorithms.
  • Software demonstrating protein secondary structure strategies
  • Exercises for protein structure predictions
  • 3D modeling of protein structures: Introduction and basis of various approaches
  • Phylogenetic Analysis: basics and demonstration.
  • Relational Databases in bioinformatics.
  • Using a relational database over the Internet: PlasmoDB.
  • Bioinformatics and micro array data analysis.

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