Bangkok, Thailand (12-15 October 2009)

The Wellcome Trust Sanger Institute Workshop

Wellcome Mahidol University, Bangkok, Thailand
Ref: ODW-Thailand


Course Summary

This 4-day Workshop is to be held at the Wellcome Mahidol University-Oxford Tropical Medicine Programme, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. It provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned. Each student will have access to a desk-top PC for the duration of the course.

This course is limited to 20 participants and will be held in English.

Sequence Formats and Retrieval:

  • DNA databases: Embl, Genbank, DDBJT
  • Protein databases: Uniprot
  • Entrez - seach sequence information, including Refseq

Genome Browsing:

  • Ensembl - full coverage including BioMart
  • VEGA
  • UCSC

De novo analysis of Sequence:

  • VEGA
  • DNA analysis - ORF finder
  • Alignment of splicing cDNA to genomic DNA - Spidey, Est2genome, SIM4
  • Multiple Sequence Alignment - CLUSTALW
  • Alignment viewing and Editing- Jalview, GeneDoc

Exploring Function and Disease:

  • Understanding Protein Function - from domains to structure (covering Pfam, InterPro, TreeFam CDD, CATH, SCOP, PDB, MSD)
  • Proteins as part of functional networks - iPfam, IntAct
  • Secondary Structure predictions
  • Disease databases COSMIC, OMIM, DECIPHER
  • Mapping disease associated SNPs to Proteins - Polyphen, SNPs 3D Rfam and microRNAs (miRBase)

Sequence Variation:

  • Ensembl SNP information, Geneview in dbSNP
  • Glovar, JSNP, HGVBase
  • Genotyping
  • Haplotypes and HapMap
  • Haploview

Comparative Sequence Analysis:

  • Homologous gene identification - Paralogues and Orthologues
  • Ensembl - orthologue prediction, MultiContigView
  • EntrezGene - BLink, Homologene
  • Comparative Genome Analysis - UCSC, Zpicture, VISTA

Example Course Manual (October 2009, Bangkok, Thailand)

An example of a course manual can be viewed and downloaded as Adobe pdf files. Click on the links below.

Module Material

Remember, modules 2 and 3 have been swapped in the running order.

Module Presentations

* quick link -